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jamestwebber/nanopore_packer_build.log

Created January 31, 2018 03:20
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Log of `PACKER_LOG=1 packer build nanopore.json`
Raw
nanopore_packer_build.log
➜ packer-images git:(specops) ✗ PACKER_LOG=1 packer build -force nanopore.json
2018/01/30 19:06:30 [INFO] Packer version: 1.1.0
2018/01/30 19:06:30 Packer Target OS/Arch: darwin amd64
2018/01/30 19:06:30 Built with Go Version: go1.9
2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 Using internal plugin for vmware-iso
2018/01/30 19:06:30 Using internal plugin for vmware-vmx
2018/01/30 19:06:30 Using internal plugin for googlecompute
2018/01/30 19:06:30 Using internal plugin for hyperv-iso
2018/01/30 19:06:30 Using internal plugin for parallels-pvm
2018/01/30 19:06:30 Using internal plugin for virtualbox-iso
2018/01/30 19:06:30 Using internal plugin for lxc
2018/01/30 19:06:30 Using internal plugin for profitbricks
2018/01/30 19:06:30 Using internal plugin for qemu
2018/01/30 19:06:30 Using internal plugin for triton
2018/01/30 19:06:30 Using internal plugin for amazon-ebs
2018/01/30 19:06:30 Using internal plugin for amazon-instance
2018/01/30 19:06:30 Using internal plugin for null
2018/01/30 19:06:30 Using internal plugin for parallels-iso
2018/01/30 19:06:30 Using internal plugin for file
2018/01/30 19:06:30 Using internal plugin for lxd
2018/01/30 19:06:30 Using internal plugin for openstack
2018/01/30 19:06:30 Using internal plugin for cloudstack
2018/01/30 19:06:30 Using internal plugin for digitalocean
2018/01/30 19:06:30 Using internal plugin for amazon-ebsvolume
2018/01/30 19:06:30 Using internal plugin for azure-arm
2018/01/30 19:06:30 Using internal plugin for docker
2018/01/30 19:06:30 Using internal plugin for oneandone
2018/01/30 19:06:30 Using internal plugin for oracle-oci
2018/01/30 19:06:30 Using internal plugin for virtualbox-ovf
2018/01/30 19:06:30 Using internal plugin for alicloud-ecs
2018/01/30 19:06:30 Using internal plugin for amazon-chroot
2018/01/30 19:06:30 Using internal plugin for amazon-ebssurrogate
2018/01/30 19:06:30 Using internal plugin for ansible
2018/01/30 19:06:30 Using internal plugin for ansible-local
2018/01/30 19:06:30 Using internal plugin for file
2018/01/30 19:06:30 Using internal plugin for shell-local
2018/01/30 19:06:30 Using internal plugin for windows-shell
2018/01/30 19:06:30 Using internal plugin for chef-solo
2018/01/30 19:06:30 Using internal plugin for puppet-server
2018/01/30 19:06:30 Using internal plugin for converge
2018/01/30 19:06:30 Using internal plugin for powershell
2018/01/30 19:06:30 Using internal plugin for salt-masterless
2018/01/30 19:06:30 Using internal plugin for shell
2018/01/30 19:06:30 Using internal plugin for windows-restart
2018/01/30 19:06:30 Using internal plugin for chef-client
2018/01/30 19:06:30 Using internal plugin for puppet-masterless
2018/01/30 19:06:30 Using internal plugin for artifice
2018/01/30 19:06:30 Using internal plugin for compress
2018/01/30 19:06:30 Using internal plugin for docker-push
2018/01/30 19:06:30 Using internal plugin for docker-save
2018/01/30 19:06:30 Using internal plugin for shell-local
2018/01/30 19:06:30 Using internal plugin for vsphere
2018/01/30 19:06:30 Using internal plugin for amazon-import
2018/01/30 19:06:30 Using internal plugin for vagrant
2018/01/30 19:06:30 Using internal plugin for vagrant-cloud
2018/01/30 19:06:30 Using internal plugin for vsphere-template
2018/01/30 19:06:30 Using internal plugin for manifest
2018/01/30 19:06:30 Using internal plugin for alicloud-import
2018/01/30 19:06:30 Using internal plugin for atlas
2018/01/30 19:06:30 Using internal plugin for checksum
2018/01/30 19:06:30 Using internal plugin for docker-import
2018/01/30 19:06:30 Using internal plugin for docker-tag
2018/01/30 19:06:30 Using internal plugin for googlecompute-export
2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 Attempting to open config file: /Users/james.webber/.packerconfig
2018/01/30 19:06:30 [WARN] Config file doesn't exist: /Users/james.webber/.packerconfig
2018/01/30 19:06:30 Packer config: &{DisableCheckpoint:false DisableCheckpointSignature:false PluginMinPort:10000 PluginMaxPort:25000 Builders:map[googlecompute:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-googlecompute hyperv-iso:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-hyperv-iso amazon-chroot:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-amazon-chroot alicloud-ecs:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-alicloud-ecs amazon-ebs:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-amazon-ebs file:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-file cloudstack:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-cloudstack docker:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-docker oracle-oci:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-oracle-oci null:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-null virtualbox-iso:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-virtualbox-iso amazon-ebssurrogate:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-amazon-ebssurrogate openstack:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-openstack digitalocean:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-digitalocean oneandone:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-oneandone virtualbox-ovf:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-virtualbox-ovf vmware-iso:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-vmware-iso vmware-vmx:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-vmware-vmx qemu:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-qemu azure-arm:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-azure-arm profitbricks:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-profitbricks amazon-instance:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-amazon-instance lxd:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-lxd parallels-iso:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-parallels-iso amazon-ebsvolume:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-amazon-ebsvolume parallels-pvm:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-parallels-pvm triton:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-triton lxc:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-builder-lxc] PostProcessors:map[googlecompute-export:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-googlecompute-export docker-save:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-docker-save vsphere-template:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-vsphere-template alicloud-import:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-alicloud-import docker-tag:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-docker-tag vagrant-cloud:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-vagrant-cloud checksum:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-checksum docker-import:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-docker-import artifice:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-artifice shell-local:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-shell-local vsphere:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-vsphere vagrant:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-vagrant compress:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-compress amazon-import:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-amazon-import manifest:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-manifest atlas:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-atlas docker-push:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-post-processor-docker-push] Provisioners:map[salt-masterless:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-salt-masterless windows-restart:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-windows-restart chef-client:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-chef-client ansible:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-ansible puppet-server:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-puppet-server converge:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-converge puppet-masterless:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-puppet-masterless file:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-file chef-solo:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-chef-solo shell-local:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-shell-local windows-shell:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-windows-shell powershell:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-powershell shell:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-shell ansible-local:/usr/local/bin/packer-PACKERSPACE-plugin-PACKERSPACE-packer-provisioner-ansible-local]}
2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 Setting cache directory: /Users/james.webber/projects/packer-images/packer_cache
2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 Loading builder: amazon-ebs
2018/01/30 19:06:30 Plugin could not be found. Checking same directory as executable.
2018/01/30 19:06:30 Current exe path: /usr/local/bin/packer
2018/01/30 19:06:30 Creating plugin client for path: /usr/local/bin/packer
2018/01/30 19:06:30 Starting plugin: /usr/local/bin/packer []string{"/usr/local/bin/packer", "plugin", "packer-builder-amazon-ebs"}
2018/01/30 19:06:30 Waiting for RPC address for: /usr/local/bin/packer
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 [INFO] Packer version: 1.1.0
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Packer Target OS/Arch: darwin amd64
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Built with Go Version: go1.9
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Attempting to open config file: /Users/james.webber/.packerconfig
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 [WARN] Config file doesn't exist: /Users/james.webber/.packerconfig
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Packer config: &{DisableCheckpoint:false DisableCheckpointSignature:false PluginMinPort:10000 PluginMaxPort:25000 Builders:map[] PostProcessors:map[] Provisioners:map[]}
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Setting cache directory: /Users/james.webber/projects/packer-images/packer_cache
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 args: []string{"packer-builder-amazon-ebs"}
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Plugin minimum port: 10000
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Plugin maximum port: 25000
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Plugin address: unix /var/folders/lg/979vjp591px7l_nyyp1w_7zhdx4x7f/T/packer-plugin697342552
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Waiting for connection...
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Serving a plugin connection...
2018/01/30 19:06:30 Loading provisioner: shell
2018/01/30 19:06:30 Plugin could not be found. Checking same directory as executable.
2018/01/30 19:06:30 Current exe path: /usr/local/bin/packer
2018/01/30 19:06:30 Creating plugin client for path: /usr/local/bin/packer
2018/01/30 19:06:30 Starting plugin: /usr/local/bin/packer []string{"/usr/local/bin/packer", "plugin", "packer-provisioner-shell"}
2018/01/30 19:06:30 Waiting for RPC address for: /usr/local/bin/packer
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 [INFO] Packer version: 1.1.0
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Packer Target OS/Arch: darwin amd64
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Built with Go Version: go1.9
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Attempting to open config file: /Users/james.webber/.packerconfig
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 [WARN] Config file doesn't exist: /Users/james.webber/.packerconfig
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Packer config: &{DisableCheckpoint:false DisableCheckpointSignature:false PluginMinPort:10000 PluginMaxPort:25000 Builders:map[] PostProcessors:map[] Provisioners:map[]}
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Setting cache directory: /Users/james.webber/projects/packer-images/packer_cache
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 args: []string{"packer-provisioner-shell"}
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Detected home directory from env var: /Users/james.webber
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Plugin minimum port: 10000
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Plugin maximum port: 25000
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Plugin address: unix /var/folders/lg/979vjp591px7l_nyyp1w_7zhdx4x7f/T/packer-plugin047222588
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Waiting for connection...
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Serving a plugin connection...
2018/01/30 19:06:30 ui: amazon-ebs output will be in this color.
2018/01/30 19:06:30 ui:
2018/01/30 19:06:30 Build debug mode: false
2018/01/30 19:06:30 Force build: true
2018/01/30 19:06:30 On error:
2018/01/30 19:06:30 Preparing build: amazon-ebs
amazon-ebs output will be in this color.
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Config: {PackerConfig:{PackerBuildName:amazon-ebs PackerBuilderType:amazon-ebs PackerDebug:false PackerForce:true PackerOnError: PackerUserVars:map[aws_region:us-west-2]} AccessConfig:{AccessKey: CustomEndpointEc2: MFACode: ProfileName: RawRegion:us-west-2 SecretKey: SkipValidation:false Token: session:<nil>} AMIConfig:{AMIName:czbiohub-nanopore-2018-01-31 AMIDescription:An Ubuntu 16.04 AMI with Albacore and Pomoxis AMIVirtType: AMIUsers:[] AMIGroups:[] AMIProductCodes:[] AMIRegions:[] AMISkipRegionValidation:false AMITags:map[Name:czbiohub-nanopore] AMIENASupport:false AMISriovNetSupport:false AMIForceDeregister:true AMIForceDeleteSnapshot:false AMIEncryptBootVolume:false AMIKmsKeyId: AMIRegionKMSKeyIDs:map[] SnapshotTags:map[] SnapshotUsers:[] SnapshotGroups:[]} BlockDevices:{AMIBlockDevices:{AMIMappings:[]} LaunchBlockDevices:{LaunchMappings:[]}} RunConfig:{AssociatePublicIpAddress:false AvailabilityZone: EbsOptimized:false IamInstanceProfile: InstanceType:m4.4xlarge RunTags:map[] SourceAmi: SourceAmiFilter:{Filters:map[0xc4204633b0:0xc4204633d0 0xc4204633f0:0xc420463410 0xc420463430:0xc420463450] Owners:[0xc4204634d0] MostRecent:true} SpotPrice: SpotPriceAutoProduct: DisableStopInstance:false SecurityGroupId: SecurityGroupIds:[] SubnetId: TemporaryKeyPairName:packer_5a7132b6-8788-b2bd-f70b-c318675157ab UserData: UserDataFile: WindowsPasswordTimeout:20m0s VpcId: InstanceInitiatedShutdownBehavior:stop Comm:{Type:ssh SSHHost: SSHPort:22 SSHUsername:ubuntu SSHPassword: SSHPrivateKey: SSHPty:false SSHTimeout:5m0s SSHAgentAuth:false SSHDisableAgentForwarding:false SSHHandshakeAttempts:10 SSHBastionHost: SSHBastionPort:0 SSHBastionAgentAuth:false SSHBastionUsername: SSHBastionPassword: SSHBastionPrivateKey: SSHFileTransferMethod:scp WinRMUser: WinRMPassword: WinRMHost: WinRMPort:0 WinRMTimeout:0s WinRMUseSSL:false WinRMInsecure:false WinRMUseNTLM:false WinRMTransportDecorator:<nil>} SSHKeyPairName: SSHPrivateIp:false} VolumeRunTags:map[] ctx:{Data:<nil> Funcs:map[clean_ami_name:0x1860380] UserVariables:map[aws_region:us-west-2] EnableEnv:false BuildName:amazon-ebs BuildType:amazon-ebs TemplatePath:/Users/james.webber/projects/packer-images/nanopore.json}}
2018/01/30 19:06:30 Waiting on builds to complete...
2018/01/30 19:06:30 Starting build run: amazon-ebs
2018/01/30 19:06:30 Running builder: amazon-ebs
2018/01/30 19:06:30 [INFO] (telemetry) Starting builder amazon-ebs
2018/01/30 19:06:30 ui: ==> amazon-ebs: Force Deregister flag found, skipping prevalidating AMI Name
==> amazon-ebs: Force Deregister flag found, skipping prevalidating AMI Name
2018/01/30 19:06:30 packer: 2018/01/30 19:06:30 Using AMI Filters {
2018/01/30 19:06:30 packer: Filters: [{
2018/01/30 19:06:30 packer: Name: "virtualization-type",
2018/01/30 19:06:30 packer: Values: ["hvm"]
2018/01/30 19:06:30 packer: },{
2018/01/30 19:06:30 packer: Name: "name",
2018/01/30 19:06:30 packer: Values: ["czbiohub-miniconda-*"]
2018/01/30 19:06:30 packer: },{
2018/01/30 19:06:30 packer: Name: "root-device-type",
2018/01/30 19:06:30 packer: Values: ["ebs"]
2018/01/30 19:06:30 packer: }],
2018/01/30 19:06:30 packer: Owners: ["423543210473"]
2018/01/30 19:06:30 packer: }
2018/01/30 19:06:31 ui: amazon-ebs: Found Image ID: ami-7861d900
amazon-ebs: Found Image ID: ami-7861d900
2018/01/30 19:06:31 ui: ==> amazon-ebs: Creating temporary keypair: packer_5a7132b6-8788-b2bd-f70b-c318675157ab
==> amazon-ebs: Creating temporary keypair: packer_5a7132b6-8788-b2bd-f70b-c318675157ab
2018/01/30 19:06:31 ui: ==> amazon-ebs: Creating temporary security group for this instance: packer_5a7132b7-5a35-933f-f0c5-214d1dd0c49a
==> amazon-ebs: Creating temporary security group for this instance: packer_5a7132b7-5a35-933f-f0c5-214d1dd0c49a
2018/01/30 19:06:31 ui: ==> amazon-ebs: Authorizing access to port 22 on the temporary security group...
==> amazon-ebs: Authorizing access to port 22 on the temporary security group...
2018/01/30 19:06:31 packer: 2018/01/30 19:06:31 [DEBUG] Waiting for temporary security group: sg-ea12d395
2018/01/30 19:06:31 packer: 2018/01/30 19:06:31 [DEBUG] Found security group sg-ea12d395
2018/01/30 19:06:31 ui: ==> amazon-ebs: Launching a source AWS instance...
==> amazon-ebs: Launching a source AWS instance...
2018/01/30 19:06:31 ui: ==> amazon-ebs: Adding tags to source instance
==> amazon-ebs: Adding tags to source instance
2018/01/30 19:06:31 ui: amazon-ebs: Adding tag: "Name": "Packer Builder"
amazon-ebs: Adding tag: "Name": "Packer Builder"
2018/01/30 19:06:32 ui: amazon-ebs: Instance ID: i-0d53c896849c06a8c
amazon-ebs: Instance ID: i-0d53c896849c06a8c
2018/01/30 19:06:32 ui: ==> amazon-ebs: Waiting for instance (i-0d53c896849c06a8c) to become ready...
2018/01/30 19:06:32 packer: 2018/01/30 19:06:32 Waiting for state to become: running
2018/01/30 19:06:32 packer: 2018/01/30 19:06:32 Using 2s as polling delay (change with AWS_POLL_DELAY_SECONDS)
==> amazon-ebs: Waiting for instance (i-0d53c896849c06a8c) to become ready...
2018/01/30 19:06:32 packer: 2018/01/30 19:06:32 Allowing 300s to complete (change with AWS_TIMEOUT_SECONDS)
2018/01/30 19:06:45 packer: 2018/01/30 19:06:45 [INFO] Not using winrm communicator, skipping get password...
2018/01/30 19:06:45 packer: 2018/01/30 19:06:45 [INFO] Waiting for SSH, up to timeout: 5m0s
2018/01/30 19:06:45 ui: ==> amazon-ebs: Waiting for SSH to become available...
==> amazon-ebs: Waiting for SSH to become available...
2018/01/30 19:07:00 packer: 2018/01/30 19:07:00 [DEBUG] TCP connection to SSH ip/port failed: dial tcp 52.37.52.221:22: i/o timeout
2018/01/30 19:07:05 packer: 2018/01/30 19:07:05 [INFO] Attempting SSH connection...
2018/01/30 19:07:05 packer: 2018/01/30 19:07:05 reconnecting to TCP connection for SSH
2018/01/30 19:07:05 packer: 2018/01/30 19:07:05 handshaking with SSH
2018/01/30 19:07:05 packer: 2018/01/30 19:07:05 handshake complete!
2018/01/30 19:07:05 packer: 2018/01/30 19:07:05 opening new ssh session
2018/01/30 19:07:06 packer: 2018/01/30 19:07:06 [INFO] agent forwarding enabled
2018/01/30 19:07:06 ui: ==> amazon-ebs: Connected to SSH!
==> amazon-ebs: Connected to SSH!
2018/01/30 19:07:06 packer: 2018/01/30 19:07:06 Running the provision hook
2018/01/30 19:07:06 [INFO] (telemetry) Starting provisioner shell
2018/01/30 19:07:06 ui: ==> amazon-ebs: Pausing 30s before the next provisioner...
==> amazon-ebs: Pausing 30s before the next provisioner...
2018/01/30 19:07:36 ui: ==> amazon-ebs: Provisioning with shell script: scripts/nanopore.sh
==> amazon-ebs: Provisioning with shell script: scripts/nanopore.sh
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 Opening scripts/nanopore.sh for reading
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 opening new ssh session
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 [INFO] 951 bytes written for 'uploadData'
2018/01/30 19:07:36 [INFO] 951 bytes written for 'uploadData'
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 Starting remote scp process: scp -vt /tmp
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 Started SCP session, beginning transfers...
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 Copying input data into temporary file so we can read the length
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 [DEBUG] scp: Uploading script_6924.sh: perms=C0644 size=951
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 SCP session complete, closing stdin pipe.
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 Waiting for SSH session to complete.
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 scp stderr (length 31): Sink: C0644 951 script_6924.sh
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 opening new ssh session
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 starting remote command: chmod 0755 /tmp/script_6924.sh
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 [INFO] RPC endpoint: Communicator ended with: 0
2018/01/30 19:07:36 [INFO] RPC client: Communicator ended with: 0
2018/01/30 19:07:36 [INFO] RPC endpoint: Communicator ended with: 0
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 [INFO] RPC client: Communicator ended with: 0
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 opening new ssh session
2018/01/30 19:07:36 packer: 2018/01/30 19:07:36 starting remote command: chmod +x /tmp/script_6924.sh; PACKER_BUILDER_TYPE='amazon-ebs' PACKER_BUILD_NAME='amazon-ebs' /tmp/script_6924.sh
2018/01/30 19:07:36 ui: amazon-ebs: + export PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: + export PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:07:36 ui: amazon-ebs: + PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: + PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:07:36 ui: amazon-ebs: + conda install virtualenv
amazon-ebs: + conda install virtualenv
amazon-ebs: Fetching package metadata .................
2018/01/30 19:07:54 ui: amazon-ebs: Fetching package metadata .................
2018/01/30 19:07:57 ui: amazon-ebs: Solving package specifications: .
amazon-ebs: Solving package specifications: .
amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs: Package plan for installation in environment /home/ubuntu/anaconda:
amazon-ebs: Package plan for installation in environment /home/ubuntu/anaconda:
2018/01/30 19:08:00 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs: The following NEW packages will be INSTALLED:
amazon-ebs: The following NEW packages will be INSTALLED:
amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs: virtualenv: 15.1.0-py36_0 conda-forge
amazon-ebs: virtualenv: 15.1.0-py36_0 conda-forge
2018/01/30 19:08:00 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs: The following packages will be SUPERSEDED by a higher-priority channel:
amazon-ebs: The following packages will be SUPERSEDED by a higher-priority channel:
2018/01/30 19:08:00 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs: conda-env: 2.6.0-h36134e3_1 --> 2.6.0-0 conda-forge
amazon-ebs: conda-env: 2.6.0-h36134e3_1 --> 2.6.0-0 conda-forge
2018/01/30 19:08:00 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:08:00 ui: amazon-ebs: conda-env-2.6. 100% |###############################| Time: 0:00:00 1.68 MB/s
amazon-ebs: conda-env-2.6. 100% |###############################| Time: 0:00:00 1.68 MB/s
2018/01/30 19:08:00 ui: amazon-ebs: virtualenv-15. 100% |###############################| Time: 0:00:01 1.41 MB/s
amazon-ebs: virtualenv-15. 100% |###############################| Time: 0:00:01 1.41 MB/s
2018/01/30 19:08:00 ui: amazon-ebs: + conda install biopython
amazon-ebs: + conda install biopython
2018/01/30 19:08:03 ui: amazon-ebs: Fetching package metadata .................
amazon-ebs: Fetching package metadata .................
2018/01/30 19:08:06 ui: amazon-ebs: Solving package specifications: .
amazon-ebs: Solving package specifications: .
amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs: Package plan for installation in environment /home/ubuntu/anaconda:
amazon-ebs: Package plan for installation in environment /home/ubuntu/anaconda:
amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs: The following NEW packages will be INSTALLED:
amazon-ebs: The following NEW packages will be INSTALLED:
2018/01/30 19:08:09 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs: biopython: 1.70-np112py36_1 bioconda
amazon-ebs: biopython: 1.70-np112py36_1 bioconda
2018/01/30 19:08:09 ui: amazon-ebs: freetype: 2.7-1 conda-forge
amazon-ebs: freetype: 2.7-1 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: intel-openmp: 2018.0.0-hc7b2577_8
amazon-ebs: intel-openmp: 2018.0.0-hc7b2577_8
2018/01/30 19:08:09 ui: amazon-ebs: jpeg: 9b-2 conda-forge
amazon-ebs: jpeg: 9b-2 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: libgfortran-ng: 7.2.0-h9f7466a_2
amazon-ebs: libgfortran-ng: 7.2.0-h9f7466a_2
2018/01/30 19:08:09 ui: amazon-ebs: libpng: 1.6.34-0 conda-forge
amazon-ebs: libpng: 1.6.34-0 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: libtiff: 4.0.9-0 conda-forge
amazon-ebs: libtiff: 4.0.9-0 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: mkl: 2018.0.1-h19d6760_4
amazon-ebs: mkl: 2018.0.1-h19d6760_4
2018/01/30 19:08:09 ui: amazon-ebs: mmtf-python: 1.0.10-py_0 conda-forge
amazon-ebs: mmtf-python: 1.0.10-py_0 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: msgpack-python: 0.5.1-py36_0 conda-forge
amazon-ebs: msgpack-python: 0.5.1-py36_0 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: numpy: 1.12.1-py36he24570b_1
amazon-ebs: numpy: 1.12.1-py36he24570b_1
2018/01/30 19:08:09 ui: amazon-ebs: olefile: 0.44-py36_0 conda-forge
amazon-ebs: olefile: 0.44-py36_0 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: pillow: 4.2.1-py36_0 conda-forge
amazon-ebs: pillow: 4.2.1-py36_0 conda-forge
2018/01/30 19:08:09 ui: amazon-ebs: reportlab: 3.4.0-py36_0 conda-forge
amazon-ebs: reportlab: 3.4.0-py36_0 conda-forge
amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs:
2018/01/30 19:08:09 ui: amazon-ebs: intel-openmp-2 100% |###############################| Time: 0:00:00 12.04 MB/s
amazon-ebs: intel-openmp-2 100% |###############################| Time: 0:00:00 12.04 MB/s
2018/01/30 19:08:09 ui: amazon-ebs: jpeg-9b-2.tar. 100% |###############################| Time: 0:00:01 880.79 kB/s
amazon-ebs: jpeg-9b-2.tar. 100% |###############################| Time: 0:00:01 880.79 kB/s
2018/01/30 19:08:09 ui: amazon-ebs: libgfortran-ng 100% |###############################| Time: 0:00:00 19.68 MB/s
amazon-ebs: libgfortran-ng 100% |###############################| Time: 0:00:00 19.68 MB/s
2018/01/30 19:08:15 ui: amazon-ebs: mkl-2018.0.1-h 100% |###############################| Time: 0:00:02 73.58 MB/s
amazon-ebs: mkl-2018.0.1-h 100% |###############################| Time: 0:00:02 73.58 MB/s
2018/01/30 19:08:15 ui: amazon-ebs: libpng-1.6.34- 100% |###############################| Time: 0:00:00 391.65 kB/s
amazon-ebs: libpng-1.6.34- 100% |###############################| Time: 0:00:00 391.65 kB/s
2018/01/30 19:08:15 ui: amazon-ebs: libtiff-4.0.9- 100% |###############################| Time: 0:00:00 655.12 kB/s
amazon-ebs: libtiff-4.0.9- 100% |###############################| Time: 0:00:00 655.12 kB/s
2018/01/30 19:08:16 ui: amazon-ebs: freetype-2.7-1 100% |###############################| Time: 0:00:01 2.19 MB/s
amazon-ebs: freetype-2.7-1 100% |###############################| Time: 0:00:01 2.19 MB/s
2018/01/30 19:08:16 ui: amazon-ebs: msgpack-python 100% |###############################| Time: 0:00:00 3.50 MB/s
amazon-ebs: msgpack-python 100% |###############################| Time: 0:00:00 3.50 MB/s
2018/01/30 19:08:20 ui: amazon-ebs: numpy-1.12.1-p 100% |###############################| Time: 0:00:00 63.13 MB/s
amazon-ebs: numpy-1.12.1-p 100% |###############################| Time: 0:00:00 63.13 MB/s
2018/01/30 19:08:20 ui: amazon-ebs: olefile-0.44-p 100% |###############################| Time: 0:00:00 592.43 kB/s
amazon-ebs: olefile-0.44-p 100% |###############################| Time: 0:00:00 592.43 kB/s
2018/01/30 19:08:20 ui: amazon-ebs: mmtf-python-1. 100% |###############################| Time: 0:00:00 250.09 kB/s
amazon-ebs: mmtf-python-1. 100% |###############################| Time: 0:00:00 250.09 kB/s
2018/01/30 19:08:20 ui: amazon-ebs: pillow-4.2.1-p 100% |###############################| Time: 0:00:01 716.83 kB/s
amazon-ebs: pillow-4.2.1-p 100% |###############################| Time: 0:00:01 716.83 kB/s
2018/01/30 19:08:22 ui: amazon-ebs: reportlab-3.4. 100% |###############################| Time: 0:00:01 1.79 MB/s
amazon-ebs: reportlab-3.4. 100% |###############################| Time: 0:00:01 1.79 MB/s
2018/01/30 19:08:58 ui: amazon-ebs: biopython-1.70 100% |###############################| Time: 0:00:00 2.78 MB/s
amazon-ebs: biopython-1.70 100% |###############################| Time: 0:00:00 2.78 MB/s
2018/01/30 19:08:58 ui: amazon-ebs: setting up albacore
amazon-ebs: setting up albacore
2018/01/30 19:08:58 ui: amazon-ebs: + echo 'setting up albacore'
amazon-ebs: + echo 'setting up albacore'
2018/01/30 19:08:58 ui: amazon-ebs: + wget -P /tmp/ https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: + wget -P /tmp/ https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:08:58 ui: amazon-ebs: --2018-01-31 03:08:58-- https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: --2018-01-31 03:08:58-- https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:08:58 ui: amazon-ebs: Resolving mirror.oxfordnanoportal.com (mirror.oxfordnanoportal.com)... 178.79.175.200, 96.126.99.215, 106.187.40.102
amazon-ebs: Resolving mirror.oxfordnanoportal.com (mirror.oxfordnanoportal.com)... 178.79.175.200, 96.126.99.215, 106.187.40.102
2018/01/30 19:08:59 ui: amazon-ebs: Connecting to mirror.oxfordnanoportal.com (mirror.oxfordnanoportal.com)|178.79.175.200|:443... connected.
amazon-ebs: Connecting to mirror.oxfordnanoportal.com (mirror.oxfordnanoportal.com)|178.79.175.200|:443... connected.
2018/01/30 19:08:59 ui: amazon-ebs: HTTP request sent, awaiting response... 301 Moved Permanently
amazon-ebs: HTTP request sent, awaiting response... 301 Moved Permanently
2018/01/30 19:08:59 ui: amazon-ebs: Location: https://americas.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl [following]
amazon-ebs: Location: https://americas.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl [following]
2018/01/30 19:08:59 ui: amazon-ebs: --2018-01-31 03:08:59-- https://americas.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: --2018-01-31 03:08:59-- https://americas.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:08:59 ui: amazon-ebs: Resolving americas.oxfordnanoportal.com (americas.oxfordnanoportal.com)... 96.126.99.215
amazon-ebs: Resolving americas.oxfordnanoportal.com (americas.oxfordnanoportal.com)... 96.126.99.215
2018/01/30 19:08:59 ui: amazon-ebs: Connecting to americas.oxfordnanoportal.com (americas.oxfordnanoportal.com)|96.126.99.215|:443... connected.
amazon-ebs: Connecting to americas.oxfordnanoportal.com (americas.oxfordnanoportal.com)|96.126.99.215|:443... connected.
2018/01/30 19:08:59 ui: amazon-ebs: HTTP request sent, awaiting response... 200 OK
amazon-ebs: HTTP request sent, awaiting response... 200 OK
2018/01/30 19:08:59 ui: amazon-ebs: Length: 13511792 (13M)
amazon-ebs: Length: 13511792 (13M)
2018/01/30 19:08:59 ui: amazon-ebs: Saving to: ‘/tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl’
amazon-ebs: Saving to: ‘/tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl’
2018/01/30 19:08:59 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:08:59 ui: amazon-ebs: 0K .......... .......... .......... .......... .......... 0% 1.98M 6s
amazon-ebs: 0K .......... .......... .......... .......... .......... 0% 1.98M 6s
2018/01/30 19:08:59 ui: amazon-ebs: 50K .......... .......... .......... .......... .......... 0% 2.43M 6s
amazon-ebs: 50K .......... .......... .......... .......... .......... 0% 2.43M 6s
2018/01/30 19:08:59 ui: amazon-ebs: 100K .......... .......... .......... .......... .......... 1% 155M 4s
amazon-ebs: 100K .......... .......... .......... .......... .......... 1% 155M 4s
2018/01/30 19:08:59 ui: amazon-ebs: 150K .......... .......... .......... .......... .......... 1% 186M 3s
amazon-ebs: 150K .......... .......... .......... .......... .......... 1% 186M 3s
2018/01/30 19:08:59 ui: amazon-ebs: 200K .......... .......... .......... .......... .......... 1% 2.48M 3s
amazon-ebs: 200K .......... .......... .......... .......... .......... 1% 2.48M 3s
2018/01/30 19:08:59 ui: amazon-ebs: 250K .......... .......... .......... .......... .......... 2% 151M 3s
amazon-ebs: 250K .......... .......... .......... .......... .......... 2% 151M 3s
2018/01/30 19:08:59 ui: amazon-ebs: 300K .......... .......... .......... .......... .......... 2% 2.51M 3s
amazon-ebs: 300K .......... .......... .......... .......... .......... 2% 2.51M 3s
2018/01/30 19:08:59 ui: amazon-ebs: 350K .......... .......... .......... .......... .......... 3% 131M 3s
amazon-ebs: 350K .......... .......... .......... .......... .......... 3% 131M 3s
2018/01/30 19:08:59 ui: amazon-ebs: 400K .......... .......... .......... .......... .......... 3% 160M 2s
amazon-ebs: 400K .......... .......... .......... .......... .......... 3% 160M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 450K .......... .......... .......... .......... .......... 3% 195M 2s
amazon-ebs: 450K .......... .......... .......... .......... .......... 3% 195M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 500K .......... .......... .......... .......... .......... 4% 214M 2s
amazon-ebs: 500K .......... .......... .......... .......... .......... 4% 214M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 550K .......... .......... .......... .......... .......... 4% 250M 2s
amazon-ebs: 550K .......... .......... .......... .......... .......... 4% 250M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 600K .......... .......... .......... .......... .......... 4% 224M 2s
amazon-ebs: 600K .......... .......... .......... .......... .......... 4% 224M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 650K .......... .......... .......... .......... .......... 5% 2.64M 2s
amazon-ebs: 650K .......... .......... .......... .......... .......... 5% 2.64M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 700K .......... .......... .......... .......... .......... 5% 122M 2s
amazon-ebs: 700K .......... .......... .......... .......... .......... 5% 122M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 750K .......... .......... .......... .......... .......... 6% 154M 2s
amazon-ebs: 750K .......... .......... .......... .......... .......... 6% 154M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 800K .......... .......... .......... .......... .......... 6% 133M 2s
amazon-ebs: 800K .......... .......... .......... .......... .......... 6% 133M 2s
2018/01/30 19:08:59 ui: amazon-ebs: 850K .......... .......... .......... .......... .......... 6% 165M 1s
amazon-ebs: 850K .......... .......... .......... .......... .......... 6% 165M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 900K .......... .......... .......... .......... .......... 7% 185M 1s
amazon-ebs: 900K .......... .......... .......... .......... .......... 7% 185M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 950K .......... .......... .......... .......... .......... 7% 214M 1s
amazon-ebs: 950K .......... .......... .......... .......... .......... 7% 214M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1000K .......... .......... .......... .......... .......... 7% 222M 1s
amazon-ebs: 1000K .......... .......... .......... .......... .......... 7% 222M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1050K .......... .......... .......... .......... .......... 8% 281M 1s
amazon-ebs: 1050K .......... .......... .......... .......... .......... 8% 281M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1100K .......... .......... .......... .......... .......... 8% 249M 1s
amazon-ebs: 1100K .......... .......... .......... .......... .......... 8% 249M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1150K .......... .......... .......... .......... .......... 9% 302M 1s
amazon-ebs: 1150K .......... .......... .......... .......... .......... 9% 302M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1200K .......... .......... .......... .......... .......... 9% 293M 1s
amazon-ebs: 1200K .......... .......... .......... .......... .......... 9% 293M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1250K .......... .......... .......... .......... .......... 9% 295M 1s
amazon-ebs: 1250K .......... .......... .......... .......... .......... 9% 295M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1300K .......... .......... .......... .......... .......... 10% 236M 1s
amazon-ebs: 1300K .......... .......... .......... .......... .......... 10% 236M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1350K .......... .......... .......... .......... .......... 10% 2.85M 1s
amazon-ebs: 1350K .......... .......... .......... .......... .......... 10% 2.85M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1400K .......... .......... .......... .......... .......... 10% 170M 1s
amazon-ebs: 1400K .......... .......... .......... .......... .......... 10% 170M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1450K .......... .......... .......... .......... .......... 11% 152M 1s
amazon-ebs: 1450K .......... .......... .......... .......... .......... 11% 152M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1500K .......... .......... .......... .......... .......... 11% 173M 1s
amazon-ebs: 1500K .......... .......... .......... .......... .......... 11% 173M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1550K .......... .......... .......... .......... .......... 12% 158M 1s
amazon-ebs: 1550K .......... .......... .......... .......... .......... 12% 158M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1600K .......... .......... .......... .......... .......... 12% 143M 1s
amazon-ebs: 1600K .......... .......... .......... .......... .......... 12% 143M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1650K .......... .......... .......... .......... .......... 12% 149M 1s
amazon-ebs: 1650K .......... .......... .......... .......... .......... 12% 149M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1700K .......... .......... .......... .......... .......... 13% 152M 1s
amazon-ebs: 1700K .......... .......... .......... .......... .......... 13% 152M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1750K .......... .......... .......... .......... .......... 13% 156M 1s
amazon-ebs: 1750K .......... .......... .......... .......... .......... 13% 156M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1800K .......... .......... .......... .......... .......... 14% 155M 1s
amazon-ebs: 1800K .......... .......... .......... .......... .......... 14% 155M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 1850K .......... .......... .......... .......... .......... 14% 223M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 1900K .......... .......... .......... .......... .......... 14% 238M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 1950K .......... .......... .......... .......... .......... 15% 244M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2000K .......... .......... .......... .......... .......... 15% 281M 1s
amazon-ebs: 2000K .......... .......... .......... .......... .......... 15% 281M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 2050K .......... .......... .......... .......... .......... 15% 229M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2100K .......... .......... .......... .......... .......... 16% 231M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2150K .......... .......... .......... .......... .......... 16% 265M 1s
amazon-ebs: 2150K .......... .......... .......... .......... .......... 16% 265M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 2200K .......... .......... .......... .......... .......... 17% 252M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2250K .......... .......... .......... .......... .......... 17% 200M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2300K .......... .......... .......... .......... .......... 17% 233M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2350K .......... .......... .......... .......... .......... 18% 238M 1s
amazon-ebs: 2350K .......... .......... .......... .......... .......... 18% 238M 1s
2018/01/30 19:08:59 ui: amazon-ebs: 2400K .......... .......... .......... .......... .......... 18% 241M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2450K .......... .......... .......... .......... .......... 18% 197M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2500K .......... .......... .......... .......... .......... 19% 243M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2550K .......... .......... .......... .......... .......... 19% 251M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2600K .......... .......... .......... .......... .......... 20% 193M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2650K .......... .......... .......... .......... .......... 20% 3.56M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2700K .......... .......... .......... .......... .......... 20% 184M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2750K .......... .......... .......... .......... .......... 21% 192M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2800K .......... .......... .......... .......... .......... 21% 131M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2850K .......... .......... .......... .......... .......... 21% 176M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2900K .......... .......... .......... .......... .......... 22% 163M 1s
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2018/01/30 19:08:59 ui: amazon-ebs: 2950K .......... .......... .......... .......... .......... 22% 147M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3000K .......... .......... .......... .......... .......... 23% 151M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3050K .......... .......... .......... .......... .......... 23% 140M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3100K .......... .......... .......... .......... .......... 23% 95.8M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3150K .......... .......... .......... .......... .......... 24% 131M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3200K .......... .......... .......... .......... .......... 24% 100M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3250K .......... .......... .......... .......... .......... 25% 219M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3300K .......... .......... .......... .......... .......... 25% 224M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3350K .......... .......... .......... .......... .......... 25% 275M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3400K .......... .......... .......... .......... .......... 26% 243M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3450K .......... .......... .......... .......... .......... 26% 264M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3500K .......... .......... .......... .......... .......... 26% 253M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3550K .......... .......... .......... .......... .......... 27% 198M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3600K .......... .......... .......... .......... .......... 27% 233M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3650K .......... .......... .......... .......... .......... 28% 242M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3700K .......... .......... .......... .......... .......... 28% 223M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3750K .......... .......... .......... .......... .......... 28% 206M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3800K .......... .......... .......... .......... .......... 29% 248M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3850K .......... .......... .......... .......... .......... 29% 230M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3900K .......... .......... .......... .......... .......... 29% 254M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 3950K .......... .......... .......... .......... .......... 30% 213M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4000K .......... .......... .......... .......... .......... 30% 274M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4050K .......... .......... .......... .......... .......... 31% 240M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4100K .......... .......... .......... .......... .......... 31% 244M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4150K .......... .......... .......... .......... .......... 31% 264M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4200K .......... .......... .......... .......... .......... 32% 256M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4250K .......... .......... .......... .......... .......... 32% 292M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4300K .......... .......... .......... .......... .......... 32% 280M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4350K .......... .......... .......... .......... .......... 33% 234M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4400K .......... .......... .......... .......... .......... 33% 283M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4450K .......... .......... .......... .......... .......... 34% 274M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4500K .......... .......... .......... .......... .......... 34% 268M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4550K .......... .......... .......... .......... .......... 34% 253M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4600K .......... .......... .......... .......... .......... 35% 286M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4650K .......... .......... .......... .......... .......... 35% 292M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4750K .......... .......... .......... .......... .......... 36% 259M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4800K .......... .......... .......... .......... .......... 36% 229M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4850K .......... .......... .......... .......... .......... 37% 241M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4900K .......... .......... .......... .......... .......... 37% 241M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 4950K .......... .......... .......... .......... .......... 37% 247M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5000K .......... .......... .......... .......... .......... 38% 228M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5050K .......... .......... .......... .......... .......... 38% 261M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5100K .......... .......... .......... .......... .......... 39% 5.30M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5150K .......... .......... .......... .......... .......... 39% 184M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5200K .......... .......... .......... .......... .......... 39% 191M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5250K .......... .......... .......... .......... .......... 40% 163M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5300K .......... .......... .......... .......... .......... 40% 187M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5350K .......... .......... .......... .......... .......... 40% 182M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5400K .......... .......... .......... .......... .......... 41% 154M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 5450K .......... .......... .......... .......... .......... 41% 208M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 7200K .......... .......... .......... .......... .......... 54% 180M 0s
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2018/01/30 19:08:59 ui: amazon-ebs: 7350K .......... .......... .......... .......... .......... 56% 187M 0s
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amazon-ebs: 12600K .......... .......... .......... .......... .......... 95% 239M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12650K .......... .......... .......... .......... .......... 96% 257M 0s
amazon-ebs: 12650K .......... .......... .......... .......... .......... 96% 257M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12700K .......... .......... .......... .......... .......... 96% 244M 0s
amazon-ebs: 12700K .......... .......... .......... .......... .......... 96% 244M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12750K .......... .......... .......... .......... .......... 97% 259M 0s
amazon-ebs: 12750K .......... .......... .......... .......... .......... 97% 259M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12800K .......... .......... .......... .......... .......... 97% 240M 0s
amazon-ebs: 12800K .......... .......... .......... .......... .......... 97% 240M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12850K .......... .......... .......... .......... .......... 97% 276M 0s
amazon-ebs: 12850K .......... .......... .......... .......... .......... 97% 276M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12900K .......... .......... .......... .......... .......... 98% 254M 0s
amazon-ebs: 12900K .......... .......... .......... .......... .......... 98% 254M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 12950K .......... .......... .......... .......... .......... 98% 272M 0s
amazon-ebs: 12950K .......... .......... .......... .......... .......... 98% 272M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 13000K .......... .......... .......... .......... .......... 98% 239M 0s
amazon-ebs: 13000K .......... .......... .......... .......... .......... 98% 239M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 13050K .......... .......... .......... .......... .......... 99% 255M 0s
amazon-ebs: 13050K .......... .......... .......... .......... .......... 99% 255M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 13100K .......... .......... .......... .......... .......... 99% 273M 0s
amazon-ebs: 13100K .......... .......... .......... .......... .......... 99% 273M 0s
2018/01/30 19:09:00 ui: amazon-ebs: 13150K .......... .......... .......... .......... ..... 100% 250M=0.2s
amazon-ebs: 13150K .......... .......... .......... .......... ..... 100% 250M=0.2s
2018/01/30 19:09:00 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:00 ui: amazon-ebs: 2018-01-31 03:08:59 (55.0 MB/s) - ‘/tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl’ saved [13511792/13511792]
amazon-ebs: 2018-01-31 03:08:59 (55.0 MB/s) - ‘/tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl’ saved [13511792/13511792]
2018/01/30 19:09:00 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:00 ui: amazon-ebs: + conda create -n albacore python=3
amazon-ebs: + conda create -n albacore python=3
2018/01/30 19:09:10 ui: amazon-ebs: Fetching package metadata .................
amazon-ebs: Fetching package metadata .................
amazon-ebs: Solving package specifications: .
2018/01/30 19:09:11 ui: amazon-ebs: Solving package specifications: .
2018/01/30 19:09:14 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:14 ui: amazon-ebs: Package plan for installation in environment /home/ubuntu/anaconda/envs/albacore:
amazon-ebs: Package plan for installation in environment /home/ubuntu/anaconda/envs/albacore:
2018/01/30 19:09:14 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:14 ui: amazon-ebs: The following NEW packages will be INSTALLED:
amazon-ebs: The following NEW packages will be INSTALLED:
2018/01/30 19:09:14 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:14 ui: amazon-ebs: ca-certificates: 2017.11.5-0 conda-forge
amazon-ebs: ca-certificates: 2017.11.5-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: certifi: 2017.11.5-py36_0 conda-forge
amazon-ebs: certifi: 2017.11.5-py36_0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: ncurses: 5.9-10 conda-forge
amazon-ebs: ncurses: 5.9-10 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: openssl: 1.0.2n-0 conda-forge
amazon-ebs: openssl: 1.0.2n-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: pip: 9.0.1-py36_1 conda-forge
amazon-ebs: pip: 9.0.1-py36_1 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: python: 3.6.4-0 conda-forge
amazon-ebs: python: 3.6.4-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: readline: 7.0-0 conda-forge
amazon-ebs: readline: 7.0-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: setuptools: 38.4.0-py36_0 conda-forge
amazon-ebs: setuptools: 38.4.0-py36_0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: sqlite: 3.20.1-2 conda-forge
amazon-ebs: sqlite: 3.20.1-2 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: tk: 8.6.7-0 conda-forge
amazon-ebs: tk: 8.6.7-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: wheel: 0.30.0-py36_2 conda-forge
amazon-ebs: wheel: 0.30.0-py36_2 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: xz: 5.2.3-0 conda-forge
amazon-ebs: xz: 5.2.3-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs: zlib: 1.2.11-0 conda-forge
amazon-ebs: zlib: 1.2.11-0 conda-forge
2018/01/30 19:09:14 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:14 ui: amazon-ebs: ncurses-5.9-10 100% |###############################| Time: 0:00:01 869.51 kB/s
amazon-ebs: ncurses-5.9-10 100% |###############################| Time: 0:00:01 869.51 kB/s
2018/01/30 19:09:15 ui: amazon-ebs: tk-8.6.7-0.tar 100% |###############################| Time: 0:00:01 2.21 MB/s
amazon-ebs: tk-8.6.7-0.tar 100% |###############################| Time: 0:00:01 2.21 MB/s
2018/01/30 19:09:17 ui: amazon-ebs: xz-5.2.3-0.tar 100% |###############################| Time: 0:00:00 4.67 MB/s
amazon-ebs: xz-5.2.3-0.tar 100% |###############################| Time: 0:00:00 4.67 MB/s
2018/01/30 19:09:17 ui: amazon-ebs: zlib-1.2.11-0. 100% |###############################| Time: 0:00:00 51.40 MB/s
amazon-ebs: zlib-1.2.11-0. 100% |###############################| Time: 0:00:00 51.40 MB/s
2018/01/30 19:09:17 ui: amazon-ebs: readline-7.0-0 100% |###############################| Time: 0:00:00 2.32 MB/s
amazon-ebs: readline-7.0-0 100% |###############################| Time: 0:00:00 2.32 MB/s
2018/01/30 19:09:18 ui: amazon-ebs: sqlite-3.20.1- 100% |###############################| Time: 0:00:00 2.90 MB/s
amazon-ebs: sqlite-3.20.1- 100% |###############################| Time: 0:00:00 2.90 MB/s
2018/01/30 19:09:20 ui: amazon-ebs: python-3.6.4-0 100% |###############################| Time: 0:00:02 8.67 MB/s
amazon-ebs: python-3.6.4-0 100% |###############################| Time: 0:00:02 8.67 MB/s
2018/01/30 19:09:20 ui: amazon-ebs: setuptools-38. 100% |###############################| Time: 0:00:00 58.84 MB/s
amazon-ebs: setuptools-38. 100% |###############################| Time: 0:00:00 58.84 MB/s
2018/01/30 19:09:21 ui: amazon-ebs: wheel-0.30.0-p 100% |###############################| Time: 0:00:00 43.67 MB/s
amazon-ebs: wheel-0.30.0-p 100% |###############################| Time: 0:00:00 43.67 MB/s
2018/01/30 19:09:27 ui: amazon-ebs: pip-9.0.1-py36 100% |###############################| Time: 0:00:00 18.51 MB/s
amazon-ebs: pip-9.0.1-py36 100% |###############################| Time: 0:00:00 18.51 MB/s
2018/01/30 19:09:27 ui: amazon-ebs: #
amazon-ebs: #
2018/01/30 19:09:27 ui: amazon-ebs: # To activate this environment, use:
amazon-ebs: # To activate this environment, use:
2018/01/30 19:09:27 ui: amazon-ebs: # > source activate albacore
amazon-ebs: # > source activate albacore
2018/01/30 19:09:27 ui: amazon-ebs: #
amazon-ebs: #
2018/01/30 19:09:27 ui: amazon-ebs: # To deactivate an active environment, use:
amazon-ebs: # To deactivate an active environment, use:
amazon-ebs: # > source deactivate
2018/01/30 19:09:27 ui: amazon-ebs: # > source deactivate
2018/01/30 19:09:27 ui: amazon-ebs: #
amazon-ebs: #
amazon-ebs:
2018/01/30 19:09:27 ui: amazon-ebs:
2018/01/30 19:09:27 ui: amazon-ebs: + source activate albacore
amazon-ebs: + source activate albacore
2018/01/30 19:09:27 ui: amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:27 ui: amazon-ebs: ++ _SCRIPT_LOCATION=/home/ubuntu/anaconda/bin/activate
amazon-ebs: ++ _SCRIPT_LOCATION=/home/ubuntu/anaconda/bin/activate
2018/01/30 19:09:27 ui: amazon-ebs: ++ _SHELL=bash
amazon-ebs: ++ _SHELL=bash
2018/01/30 19:09:27 ui: amazon-ebs: +++ dirname /home/ubuntu/anaconda/bin/activate
amazon-ebs: +++ dirname /home/ubuntu/anaconda/bin/activate
2018/01/30 19:09:27 ui: amazon-ebs: ++ _CONDA_DIR=/home/ubuntu/anaconda/bin
amazon-ebs: ++ _CONDA_DIR=/home/ubuntu/anaconda/bin
2018/01/30 19:09:27 ui: amazon-ebs: ++ '[' 1 -gt 1 ']'
amazon-ebs: ++ '[' 1 -gt 1 ']'
2018/01/30 19:09:27 ui: amazon-ebs: ++ case "$(uname -s)" in
amazon-ebs: ++ case "$(uname -s)" in
2018/01/30 19:09:27 ui: amazon-ebs: +++ uname -s
amazon-ebs: +++ uname -s
2018/01/30 19:09:27 ui: amazon-ebs: ++ EXT=
amazon-ebs: ++ EXT=
2018/01/30 19:09:27 ui: amazon-ebs: ++ export _CONDA_PYTHON=/home/ubuntu/anaconda/bin/python
amazon-ebs: ++ export _CONDA_PYTHON=/home/ubuntu/anaconda/bin/python
2018/01/30 19:09:27 ui: amazon-ebs: ++ _CONDA_PYTHON=/home/ubuntu/anaconda/bin/python
amazon-ebs: ++ _CONDA_PYTHON=/home/ubuntu/anaconda/bin/python
2018/01/30 19:09:27 ui: amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ basename /tmp/script_6924.sh
amazon-ebs: +++ basename /tmp/script_6924.sh
2018/01/30 19:09:27 ui: amazon-ebs: ++ [[ script_6924.sh == \a\c\t\i\v\a\t\e ]]
amazon-ebs: ++ [[ script_6924.sh == \a\c\t\i\v\a\t\e ]]
2018/01/30 19:09:27 ui: amazon-ebs: ++ '[' 1 -eq 0 ']'
amazon-ebs: ++ '[' 1 -eq 0 ']'
2018/01/30 19:09:27 ui: amazon-ebs: ++ args=albacore
amazon-ebs: ++ args=albacore
2018/01/30 19:09:27 ui: amazon-ebs: ++ /home/ubuntu/anaconda/bin/conda ..checkenv bash albacore
amazon-ebs: ++ /home/ubuntu/anaconda/bin/conda ..checkenv bash albacore
2018/01/30 19:09:27 ui: amazon-ebs: ++ (( 0 != 0 ))
amazon-ebs: ++ (( 0 != 0 ))
2018/01/30 19:09:27 ui: amazon-ebs: ++ _CONDA_HOLD=true
amazon-ebs: ++ _CONDA_HOLD=true
2018/01/30 19:09:27 ui: amazon-ebs: ++ source /home/ubuntu/anaconda/bin/deactivate
amazon-ebs: ++ source /home/ubuntu/anaconda/bin/deactivate
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: +++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ _SCRIPT_LOCATION=/home/ubuntu/anaconda/bin/deactivate
amazon-ebs: +++ _SCRIPT_LOCATION=/home/ubuntu/anaconda/bin/deactivate
2018/01/30 19:09:27 ui: amazon-ebs: +++ _SHELL=bash
amazon-ebs: +++ _SHELL=bash
2018/01/30 19:09:27 ui: amazon-ebs: ++++ dirname /home/ubuntu/anaconda/bin/deactivate
amazon-ebs: ++++ dirname /home/ubuntu/anaconda/bin/deactivate
2018/01/30 19:09:27 ui: amazon-ebs: +++ _CONDA_DIR=/home/ubuntu/anaconda/bin
amazon-ebs: +++ _CONDA_DIR=/home/ubuntu/anaconda/bin
2018/01/30 19:09:27 ui: amazon-ebs: +++ case "$(uname -s)" in
amazon-ebs: +++ case "$(uname -s)" in
2018/01/30 19:09:27 ui: amazon-ebs: ++++ uname -s
amazon-ebs: ++++ uname -s
2018/01/30 19:09:27 ui: amazon-ebs: +++ EXT=
amazon-ebs: +++ EXT=
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ 1 > 0 ]]
amazon-ebs: +++ [[ 1 > 0 ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ key=albacore
amazon-ebs: +++ key=albacore
2018/01/30 19:09:27 ui: amazon-ebs: +++ case $key in
amazon-ebs: +++ case $key in
2018/01/30 19:09:27 ui: amazon-ebs: +++ shift
amazon-ebs: +++ shift
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ 0 > 0 ]]
amazon-ebs: +++ [[ 0 > 0 ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: +++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:27 ui: amazon-ebs: ++++ basename /tmp/script_6924.sh
amazon-ebs: ++++ basename /tmp/script_6924.sh
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ script_6924.sh == \d\e\a\c\t\i\v\a\t\e ]]
amazon-ebs: +++ [[ script_6924.sh == \d\e\a\c\t\i\v\a\t\e ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ -z '' ]]
amazon-ebs: +++ [[ -z '' ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: +++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:27 ui: amazon-ebs: ++++ basename /tmp/script_6924.sh
amazon-ebs: ++++ basename /tmp/script_6924.sh
2018/01/30 19:09:27 ui: amazon-ebs: +++ [[ script_6924.sh == \d\e\a\c\t\i\v\a\t\e ]]
amazon-ebs: +++ [[ script_6924.sh == \d\e\a\c\t\i\v\a\t\e ]]
2018/01/30 19:09:27 ui: amazon-ebs: +++ return 0
amazon-ebs: +++ return 0
2018/01/30 19:09:27 ui: amazon-ebs: ++ unset _CONDA_HOLD
amazon-ebs: ++ unset _CONDA_HOLD
2018/01/30 19:09:27 ui: amazon-ebs: +++ /home/ubuntu/anaconda/bin/conda ..activate bash albacore
amazon-ebs: +++ /home/ubuntu/anaconda/bin/conda ..activate bash albacore
2018/01/30 19:09:27 ui: amazon-ebs: ++ _NEW_PART=/home/ubuntu/anaconda/envs/albacore/bin
amazon-ebs: ++ _NEW_PART=/home/ubuntu/anaconda/envs/albacore/bin
2018/01/30 19:09:27 ui: amazon-ebs: ++ (( 0 == 0 ))
amazon-ebs: ++ (( 0 == 0 ))
2018/01/30 19:09:27 ui: amazon-ebs: ++ export CONDA_PATH_BACKUP=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: ++ export CONDA_PATH_BACKUP=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:09:27 ui: amazon-ebs: ++ CONDA_PATH_BACKUP=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: ++ CONDA_PATH_BACKUP=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:09:27 ui: amazon-ebs: ++ export CONDA_PS1_BACKUP=
amazon-ebs: ++ export CONDA_PS1_BACKUP=
2018/01/30 19:09:27 ui: amazon-ebs: ++ CONDA_PS1_BACKUP=
amazon-ebs: ++ CONDA_PS1_BACKUP=
2018/01/30 19:09:27 ui: amazon-ebs: ++ [[ /home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]]
amazon-ebs: ++ [[ /home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]]
2018/01/30 19:09:27 ui: amazon-ebs: ++ export PATH=/home/ubuntu/anaconda/envs/albacore/bin:/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:09:27 ui: amazon-ebs: ++ PATH=/home/ubuntu/anaconda/envs/albacore/bin:/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: ++ export PATH=/home/ubuntu/anaconda/envs/albacore/bin:/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:09:27 ui: amazon-ebs: ++ [[ '' == */* ]]
amazon-ebs: ++ PATH=/home/ubuntu/anaconda/envs/albacore/bin:/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: ++ [[ '' == */* ]]
2018/01/30 19:09:27 ui: amazon-ebs: ++ export CONDA_DEFAULT_ENV=albacore
amazon-ebs: ++ export CONDA_DEFAULT_ENV=albacore
2018/01/30 19:09:27 ui: amazon-ebs: ++ CONDA_DEFAULT_ENV=albacore
amazon-ebs: ++ CONDA_DEFAULT_ENV=albacore
2018/01/30 19:09:27 ui: amazon-ebs: ++ firstpath=/home/ubuntu/anaconda/envs/albacore/bin
amazon-ebs: ++ firstpath=/home/ubuntu/anaconda/envs/albacore/bin
2018/01/30 19:09:27 ui: amazon-ebs: +++ echo /home/ubuntu/anaconda/envs/albacore/bin
amazon-ebs: +++ echo /home/ubuntu/anaconda/envs/albacore/bin
2018/01/30 19:09:27 ui: amazon-ebs: +++ sed 's|/bin$||'
amazon-ebs: +++ sed 's|/bin$||'
2018/01/30 19:09:27 ui: amazon-ebs: ++ export CONDA_PREFIX=/home/ubuntu/anaconda/envs/albacore
amazon-ebs: ++ export CONDA_PREFIX=/home/ubuntu/anaconda/envs/albacore
2018/01/30 19:09:27 ui: amazon-ebs: +++ /home/ubuntu/anaconda/bin/conda ..changeps1
amazon-ebs: +++ /home/ubuntu/anaconda/bin/conda ..changeps1
2018/01/30 19:09:28 ui: amazon-ebs: ++ '[' 0 = 1 ']'
amazon-ebs: ++ '[' 0 = 1 ']'
2018/01/30 19:09:28 ui: amazon-ebs: ++ _CONDA_D=/home/ubuntu/anaconda/envs/albacore/etc/conda/activate.d
amazon-ebs: ++ _CONDA_D=/home/ubuntu/anaconda/envs/albacore/etc/conda/activate.d
2018/01/30 19:09:28 ui: amazon-ebs: ++ [[ -d /home/ubuntu/anaconda/envs/albacore/etc/conda/activate.d ]]
amazon-ebs: ++ [[ -d /home/ubuntu/anaconda/envs/albacore/etc/conda/activate.d ]]
2018/01/30 19:09:28 ui: amazon-ebs: ++ unset _CONDA_PYTHON
amazon-ebs: ++ unset _CONDA_PYTHON
2018/01/30 19:09:28 ui: amazon-ebs: ++ unset CONDA_PATH
amazon-ebs: ++ unset CONDA_PATH
2018/01/30 19:09:28 ui: amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:28 ui: amazon-ebs: ++ hash -r
amazon-ebs: ++ hash -r
2018/01/30 19:09:28 ui: amazon-ebs: + pip install /tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: + pip install /tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:09:28 ui: amazon-ebs: Processing /tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: Processing /tmp/ont_albacore-2.1.3-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:09:29 ui: amazon-ebs: Collecting numpy>=1.13.3 (from ont-albacore==2.1.3)
amazon-ebs: Collecting numpy>=1.13.3 (from ont-albacore==2.1.3)
2018/01/30 19:09:29 ui: amazon-ebs: Downloading numpy-1.14.0-cp36-cp36m-manylinux1_x86_64.whl (17.2MB)
amazon-ebs: Downloading numpy-1.14.0-cp36-cp36m-manylinux1_x86_64.whl (17.2MB)
2018/01/30 19:09:32 ui: amazon-ebs: Collecting progressbar33 (from ont-albacore==2.1.3)
amazon-ebs: Collecting progressbar33 (from ont-albacore==2.1.3)
2018/01/30 19:09:33 ui: amazon-ebs: Downloading progressbar33-2.4.tar.gz
amazon-ebs: Downloading progressbar33-2.4.tar.gz
2018/01/30 19:09:33 ui: amazon-ebs: Collecting ont-fast5-api>=0.4.1 (from ont-albacore==2.1.3)
amazon-ebs: Collecting ont-fast5-api>=0.4.1 (from ont-albacore==2.1.3)
2018/01/30 19:09:33 ui: amazon-ebs: Downloading ont_fast5_api-0.4.1-py2.py3-none-any.whl
amazon-ebs: Downloading ont_fast5_api-0.4.1-py2.py3-none-any.whl
2018/01/30 19:09:33 ui: amazon-ebs: Collecting python-dateutil (from ont-albacore==2.1.3)
amazon-ebs: Collecting python-dateutil (from ont-albacore==2.1.3)
2018/01/30 19:09:33 ui: amazon-ebs: Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
amazon-ebs: Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
2018/01/30 19:09:33 ui: amazon-ebs: Collecting h5py (from ont-albacore==2.1.3)
amazon-ebs: Collecting h5py (from ont-albacore==2.1.3)
2018/01/30 19:09:33 ui: amazon-ebs: Downloading h5py-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (5.4MB)
amazon-ebs: Downloading h5py-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (5.4MB)
2018/01/30 19:09:34 ui: amazon-ebs: Requirement already satisfied: setuptools in ./anaconda/envs/albacore/lib/python3.6/site-packages (from ont-albacore==2.1.3)
amazon-ebs: Requirement already satisfied: setuptools in ./anaconda/envs/albacore/lib/python3.6/site-packages (from ont-albacore==2.1.3)
2018/01/30 19:09:34 ui: amazon-ebs: Collecting six>=1.5 (from python-dateutil->ont-albacore==2.1.3)
amazon-ebs: Collecting six>=1.5 (from python-dateutil->ont-albacore==2.1.3)
2018/01/30 19:09:34 ui: amazon-ebs: Downloading six-1.11.0-py2.py3-none-any.whl
amazon-ebs: Downloading six-1.11.0-py2.py3-none-any.whl
2018/01/30 19:09:34 ui: amazon-ebs: Building wheels for collected packages: progressbar33
amazon-ebs: Building wheels for collected packages: progressbar33
2018/01/30 19:09:34 ui: amazon-ebs: Running setup.py bdist_wheel for progressbar33: started
amazon-ebs: Running setup.py bdist_wheel for progressbar33: started
2018/01/30 19:09:34 ui: amazon-ebs: Running setup.py bdist_wheel for progressbar33: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for progressbar33: finished with status 'done'
2018/01/30 19:09:34 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/4d/72/a3/a74877f299ef2e9bed86e29ab723bd5adfe7cef6f1d0cfa986
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/4d/72/a3/a74877f299ef2e9bed86e29ab723bd5adfe7cef6f1d0cfa986
2018/01/30 19:09:34 ui: amazon-ebs: Successfully built progressbar33
amazon-ebs: Successfully built progressbar33
2018/01/30 19:09:34 ui: amazon-ebs: Installing collected packages: numpy, progressbar33, six, h5py, ont-fast5-api, python-dateutil, ont-albacore
amazon-ebs: Installing collected packages: numpy, progressbar33, six, h5py, ont-fast5-api, python-dateutil, ont-albacore
2018/01/30 19:09:36 ui: amazon-ebs: Successfully installed h5py-2.7.1 numpy-1.14.0 ont-albacore-2.1.3 ont-fast5-api-0.4.1 progressbar33-2.4 python-dateutil-2.6.1 six-1.11.0
amazon-ebs: Successfully installed h5py-2.7.1 numpy-1.14.0 ont-albacore-2.1.3 ont-fast5-api-0.4.1 progressbar33-2.4 python-dateutil-2.6.1 six-1.11.0
2018/01/30 19:09:36 ui: amazon-ebs: + source deactivate
amazon-ebs: + source deactivate
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:36 ui: amazon-ebs: ++ _SCRIPT_LOCATION=/home/ubuntu/anaconda/envs/albacore/bin/deactivate
amazon-ebs: ++ _SCRIPT_LOCATION=/home/ubuntu/anaconda/envs/albacore/bin/deactivate
2018/01/30 19:09:36 ui: amazon-ebs: ++ _SHELL=bash
amazon-ebs: ++ _SHELL=bash
2018/01/30 19:09:36 ui: amazon-ebs: +++ dirname /home/ubuntu/anaconda/envs/albacore/bin/deactivate
amazon-ebs: +++ dirname /home/ubuntu/anaconda/envs/albacore/bin/deactivate
2018/01/30 19:09:36 ui: amazon-ebs: ++ _CONDA_DIR=/home/ubuntu/anaconda/envs/albacore/bin
amazon-ebs: ++ _CONDA_DIR=/home/ubuntu/anaconda/envs/albacore/bin
2018/01/30 19:09:36 ui: amazon-ebs: ++ case "$(uname -s)" in
amazon-ebs: ++ case "$(uname -s)" in
2018/01/30 19:09:36 ui: amazon-ebs: +++ uname -s
amazon-ebs: +++ uname -s
2018/01/30 19:09:36 ui: amazon-ebs: ++ EXT=
amazon-ebs: ++ EXT=
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ 0 > 0 ]]
amazon-ebs: ++ [[ 0 > 0 ]]
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:36 ui: amazon-ebs: +++ basename /tmp/script_6924.sh
amazon-ebs: +++ basename /tmp/script_6924.sh
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ script_6924.sh == \d\e\a\c\t\i\v\a\t\e ]]
amazon-ebs: ++ [[ script_6924.sh == \d\e\a\c\t\i\v\a\t\e ]]
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ -z /home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]
amazon-ebs: ++ [[ -z /home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]
2018/01/30 19:09:36 ui: amazon-ebs: ++ (( 0 == 0 ))
amazon-ebs: ++ (( 0 == 0 ))
2018/01/30 19:09:36 ui: amazon-ebs: ++ _CONDA_D=/home/ubuntu/anaconda/envs/albacore/etc/conda/deactivate.d
amazon-ebs: ++ _CONDA_D=/home/ubuntu/anaconda/envs/albacore/etc/conda/deactivate.d
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ -d /home/ubuntu/anaconda/envs/albacore/etc/conda/deactivate.d ]]
amazon-ebs: ++ [[ -d /home/ubuntu/anaconda/envs/albacore/etc/conda/deactivate.d ]]
2018/01/30 19:09:36 ui: amazon-ebs: +++ /home/ubuntu/anaconda/envs/albacore/bin/conda ..deactivate.path bash /home/ubuntu/anaconda/envs/albacore
amazon-ebs: +++ /home/ubuntu/anaconda/envs/albacore/bin/conda ..deactivate.path bash /home/ubuntu/anaconda/envs/albacore
2018/01/30 19:09:36 ui: amazon-ebs: ++ export PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: ++ export PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:09:36 ui: amazon-ebs: ++ PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
amazon-ebs: ++ PATH=/home/ubuntu/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
2018/01/30 19:09:36 ui: amazon-ebs: ++ unset CONDA_DEFAULT_ENV
amazon-ebs: ++ unset CONDA_DEFAULT_ENV
2018/01/30 19:09:36 ui: amazon-ebs: ++ unset CONDA_PREFIX
amazon-ebs: ++ unset CONDA_PREFIX
2018/01/30 19:09:36 ui: amazon-ebs: done with albacore setup
amazon-ebs: done with albacore setup
2018/01/30 19:09:36 ui: amazon-ebs: ++ unset CONDA_PATH_BACKUP
amazon-ebs: ++ unset CONDA_PATH_BACKUP
2018/01/30 19:09:36 ui: amazon-ebs: ++ export PS1=
amazon-ebs: ++ export PS1=
2018/01/30 19:09:36 ui: amazon-ebs: Filesystem Size Used Avail Use% Mounted on
amazon-ebs: Filesystem Size Used Avail Use% Mounted on
2018/01/30 19:09:36 ui: amazon-ebs: ++ PS1=
amazon-ebs: ++ PS1=
2018/01/30 19:09:36 ui: amazon-ebs: ++ unset CONDA_PS1_BACKUP
amazon-ebs: ++ unset CONDA_PS1_BACKUP
2018/01/30 19:09:36 ui: amazon-ebs: ++ unset _CONDA_PYTHON2
amazon-ebs: ++ unset _CONDA_PYTHON2
2018/01/30 19:09:36 ui: amazon-ebs: udev 32G 0 32G 0% /dev
amazon-ebs: udev 32G 0 32G 0% /dev
2018/01/30 19:09:36 ui: amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
amazon-ebs: ++ [[ -n 4.3.48(1)-release ]]
2018/01/30 19:09:36 ui: amazon-ebs: ++ hash -r
amazon-ebs: ++ hash -r
2018/01/30 19:09:36 ui: amazon-ebs: + echo 'done with albacore setup'
amazon-ebs: + echo 'done with albacore setup'
2018/01/30 19:09:36 ui: amazon-ebs: + df -h
amazon-ebs: + df -h
2018/01/30 19:09:36 ui: amazon-ebs: tmpfs 6.3G 8.6M 6.3G 1% /run
amazon-ebs: tmpfs 6.3G 8.6M 6.3G 1% /run
2018/01/30 19:09:36 ui: amazon-ebs: /dev/xvda1 7.7G 2.9G 4.9G 38% /
amazon-ebs: /dev/xvda1 7.7G 2.9G 4.9G 38% /
2018/01/30 19:09:36 ui: amazon-ebs: tmpfs 32G 0 32G 0% /dev/shm
amazon-ebs: tmpfs 32G 0 32G 0% /dev/shm
2018/01/30 19:09:36 ui: amazon-ebs: tmpfs 5.0M 0 5.0M 0% /run/lock
amazon-ebs: tmpfs 5.0M 0 5.0M 0% /run/lock
2018/01/30 19:09:36 ui: amazon-ebs: + echo 'installing pomoxis dependencies'
amazon-ebs: + echo 'installing pomoxis dependencies'
amazon-ebs: + yes
2018/01/30 19:09:36 ui: amazon-ebs: + yes
2018/01/30 19:09:36 ui: amazon-ebs: + sudo apt-get install libz-dev
amazon-ebs: + sudo apt-get install libz-dev
2018/01/30 19:09:36 ui: amazon-ebs: tmpfs 32G 0 32G 0% /sys/fs/cgroup
amazon-ebs: tmpfs 32G 0 32G 0% /sys/fs/cgroup
2018/01/30 19:09:36 ui: amazon-ebs: tmpfs 6.3G 0 6.3G 0% /run/user/1000
amazon-ebs: tmpfs 6.3G 0 6.3G 0% /run/user/1000
2018/01/30 19:09:36 ui: amazon-ebs: installing pomoxis dependencies
amazon-ebs: installing pomoxis dependencies
2018/01/30 19:09:38 ui: amazon-ebs: Reading package lists...
amazon-ebs: Reading package lists...
2018/01/30 19:09:38 ui: amazon-ebs: Building dependency tree...
amazon-ebs: Building dependency tree...
2018/01/30 19:09:38 ui: amazon-ebs: Reading state information...
amazon-ebs: Reading state information...
2018/01/30 19:09:38 ui: amazon-ebs: The following NEW packages will be installed:
amazon-ebs: The following NEW packages will be installed:
2018/01/30 19:09:38 ui: amazon-ebs: zlib1g-dev
amazon-ebs: zlib1g-dev
2018/01/30 19:09:38 ui: amazon-ebs: 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
amazon-ebs: 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
2018/01/30 19:09:38 ui: amazon-ebs: Need to get 168 kB of archives.
amazon-ebs: Need to get 168 kB of archives.
2018/01/30 19:09:38 ui: amazon-ebs: After this operation, 425 kB of additional disk space will be used.
amazon-ebs: After this operation, 425 kB of additional disk space will be used.
2018/01/30 19:09:38 ui: amazon-ebs: Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2ubuntu4.1 [168 kB]
amazon-ebs: Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2ubuntu4.1 [168 kB]
2018/01/30 19:09:38 ui: amazon-ebs: debconf: unable to initialize frontend: Dialog
amazon-ebs: debconf: unable to initialize frontend: Dialog
2018/01/30 19:09:38 ui: amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
2018/01/30 19:09:38 ui: amazon-ebs: debconf: falling back to frontend: Readline
amazon-ebs: debconf: falling back to frontend: Readline
2018/01/30 19:09:38 ui: amazon-ebs: debconf: unable to initialize frontend: Readline
amazon-ebs: debconf: unable to initialize frontend: Readline
2018/01/30 19:09:38 ui: amazon-ebs: debconf: (This frontend requires a controlling tty.)
amazon-ebs: debconf: (This frontend requires a controlling tty.)
2018/01/30 19:09:38 ui: amazon-ebs: debconf: falling back to frontend: Teletype
amazon-ebs: debconf: falling back to frontend: Teletype
2018/01/30 19:09:38 ui: amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
2018/01/30 19:09:38 ui: amazon-ebs: Fetched 168 kB in 0s (11.9 MB/s)
amazon-ebs: Fetched 168 kB in 0s (11.9 MB/s)
2018/01/30 19:09:38 ui: amazon-ebs: Selecting previously unselected package zlib1g-dev:amd64.
amazon-ebs: Selecting previously unselected package zlib1g-dev:amd64.
2018/01/30 19:09:39 ui: amazon-ebs: (Reading database ... 58291 files and directories currently installed.)
amazon-ebs: (Reading database ... 58291 files and directories currently installed.)
2018/01/30 19:09:39 ui: amazon-ebs: Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu4.1_amd64.deb ...
amazon-ebs: Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu4.1_amd64.deb ...
2018/01/30 19:09:39 ui: amazon-ebs: Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4.1) ...
amazon-ebs: Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4.1) ...
2018/01/30 19:09:39 ui: amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
2018/01/30 19:09:39 ui: amazon-ebs: Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4.1) ...
amazon-ebs: Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4.1) ...
amazon-ebs: + yes
2018/01/30 19:09:40 ui: amazon-ebs: + yes
2018/01/30 19:09:40 ui: amazon-ebs: + sudo apt-get install libncurses5-dev
amazon-ebs: + sudo apt-get install libncurses5-dev
2018/01/30 19:09:40 ui: amazon-ebs: Reading package lists...
amazon-ebs: Reading package lists...
2018/01/30 19:09:40 ui: amazon-ebs: Building dependency tree...
amazon-ebs: Building dependency tree...
2018/01/30 19:09:40 ui: amazon-ebs: Reading state information...
amazon-ebs: Reading state information...
2018/01/30 19:09:40 ui: amazon-ebs: The following additional packages will be installed:
amazon-ebs: The following additional packages will be installed:
2018/01/30 19:09:40 ui: amazon-ebs: libtinfo-dev
amazon-ebs: libtinfo-dev
2018/01/30 19:09:40 ui: amazon-ebs: Suggested packages:
amazon-ebs: Suggested packages:
2018/01/30 19:09:40 ui: amazon-ebs: ncurses-doc
amazon-ebs: ncurses-doc
2018/01/30 19:09:40 ui: amazon-ebs: The following NEW packages will be installed:
amazon-ebs: The following NEW packages will be installed:
2018/01/30 19:09:40 ui: amazon-ebs: libncurses5-dev libtinfo-dev
amazon-ebs: libncurses5-dev libtinfo-dev
2018/01/30 19:09:40 ui: amazon-ebs: 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
amazon-ebs: 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
2018/01/30 19:09:40 ui: amazon-ebs: Need to get 252 kB of archives.
amazon-ebs: Need to get 252 kB of archives.
2018/01/30 19:09:40 ui: amazon-ebs: After this operation, 1,461 kB of additional disk space will be used.
amazon-ebs: After this operation, 1,461 kB of additional disk space will be used.
2018/01/30 19:09:40 ui: amazon-ebs: Do you want to continue? [Y/n] Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libtinfo-dev amd64 6.0+20160213-1ubuntu1 [77.4 kB]
amazon-ebs: Do you want to continue? [Y/n] Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libtinfo-dev amd64 6.0+20160213-1ubuntu1 [77.4 kB]
2018/01/30 19:09:40 ui: amazon-ebs: Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libncurses5-dev amd64 6.0+20160213-1ubuntu1 [175 kB]
amazon-ebs: Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libncurses5-dev amd64 6.0+20160213-1ubuntu1 [175 kB]
2018/01/30 19:09:41 ui: amazon-ebs: debconf: unable to initialize frontend: Dialog
amazon-ebs: debconf: unable to initialize frontend: Dialog
2018/01/30 19:09:41 ui: amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
2018/01/30 19:09:41 ui: amazon-ebs: debconf: falling back to frontend: Readline
amazon-ebs: debconf: falling back to frontend: Readline
2018/01/30 19:09:41 ui: amazon-ebs: debconf: unable to initialize frontend: Readline
amazon-ebs: debconf: unable to initialize frontend: Readline
2018/01/30 19:09:41 ui: amazon-ebs: debconf: (This frontend requires a controlling tty.)
amazon-ebs: debconf: (This frontend requires a controlling tty.)
2018/01/30 19:09:41 ui: amazon-ebs: debconf: falling back to frontend: Teletype
amazon-ebs: debconf: falling back to frontend: Teletype
2018/01/30 19:09:41 ui: amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
2018/01/30 19:09:41 ui: amazon-ebs: Fetched 252 kB in 0s (24.0 MB/s)
amazon-ebs: Fetched 252 kB in 0s (24.0 MB/s)
2018/01/30 19:09:41 ui: amazon-ebs: Selecting previously unselected package libtinfo-dev:amd64.
amazon-ebs: Selecting previously unselected package libtinfo-dev:amd64.
2018/01/30 19:09:41 ui: amazon-ebs: (Reading database ... 58320 files and directories currently installed.)
2018/01/30 19:09:41 ui: amazon-ebs: Preparing to unpack .../libtinfo-dev_6.0+20160213-1ubuntu1_amd64.deb ...
amazon-ebs: (Reading database ... 58320 files and directories currently installed.)
amazon-ebs: Preparing to unpack .../libtinfo-dev_6.0+20160213-1ubuntu1_amd64.deb ...
2018/01/30 19:09:41 ui: amazon-ebs: Unpacking libtinfo-dev:amd64 (6.0+20160213-1ubuntu1) ...
amazon-ebs: Unpacking libtinfo-dev:amd64 (6.0+20160213-1ubuntu1) ...
2018/01/30 19:09:41 ui: amazon-ebs: Selecting previously unselected package libncurses5-dev:amd64.
amazon-ebs: Selecting previously unselected package libncurses5-dev:amd64.
2018/01/30 19:09:41 ui: amazon-ebs: Preparing to unpack .../libncurses5-dev_6.0+20160213-1ubuntu1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libncurses5-dev_6.0+20160213-1ubuntu1_amd64.deb ...
2018/01/30 19:09:41 ui: amazon-ebs: Unpacking libncurses5-dev:amd64 (6.0+20160213-1ubuntu1) ...
amazon-ebs: Unpacking libncurses5-dev:amd64 (6.0+20160213-1ubuntu1) ...
2018/01/30 19:09:41 ui: amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
2018/01/30 19:09:41 ui: amazon-ebs: Setting up libtinfo-dev:amd64 (6.0+20160213-1ubuntu1) ...
amazon-ebs: Setting up libtinfo-dev:amd64 (6.0+20160213-1ubuntu1) ...
2018/01/30 19:09:41 ui: amazon-ebs: Setting up libncurses5-dev:amd64 (6.0+20160213-1ubuntu1) ...
amazon-ebs: Setting up libncurses5-dev:amd64 (6.0+20160213-1ubuntu1) ...
2018/01/30 19:09:42 ui: amazon-ebs: + yes
amazon-ebs: + yes
2018/01/30 19:09:42 ui: amazon-ebs: + sudo apt-get install libhdf5-dev
amazon-ebs: + sudo apt-get install libhdf5-dev
2018/01/30 19:09:42 ui: amazon-ebs: Reading package lists...
amazon-ebs: Reading package lists...
2018/01/30 19:09:42 ui: amazon-ebs: Building dependency tree...
amazon-ebs: Building dependency tree...
2018/01/30 19:09:42 ui: amazon-ebs: Reading state information...
amazon-ebs: Reading state information...
2018/01/30 19:09:42 ui: amazon-ebs: The following additional packages will be installed:
amazon-ebs: The following additional packages will be installed:
2018/01/30 19:09:42 ui: amazon-ebs: hdf5-helpers libaec-dev libaec0 libgfortran3 libhdf5-10 libhdf5-cpp-11
amazon-ebs: hdf5-helpers libaec-dev libaec0 libgfortran3 libhdf5-10 libhdf5-cpp-11
2018/01/30 19:09:42 ui: amazon-ebs: libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libsz2
amazon-ebs: libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libsz2
2018/01/30 19:09:42 ui: amazon-ebs: Suggested packages:
amazon-ebs: Suggested packages:
2018/01/30 19:09:42 ui: amazon-ebs: libhdf5-doc
amazon-ebs: libhdf5-doc
2018/01/30 19:09:42 ui: amazon-ebs: The following NEW packages will be installed:
amazon-ebs: The following NEW packages will be installed:
2018/01/30 19:09:42 ui: amazon-ebs: hdf5-helpers libaec-dev libaec0 libgfortran3 libhdf5-10 libhdf5-cpp-11
amazon-ebs: hdf5-helpers libaec-dev libaec0 libgfortran3 libhdf5-10 libhdf5-cpp-11
2018/01/30 19:09:42 ui: amazon-ebs: libhdf5-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libsz2
amazon-ebs: libhdf5-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libsz2
2018/01/30 19:09:42 ui: amazon-ebs: 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
amazon-ebs: 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
2018/01/30 19:09:42 ui: amazon-ebs: Need to get 6,670 kB of archives.
amazon-ebs: Need to get 6,670 kB of archives.
2018/01/30 19:09:42 ui: amazon-ebs: After this operation, 37.4 MB of additional disk space will be used.
amazon-ebs: After this operation, 37.4 MB of additional disk space will be used.
2018/01/30 19:09:42 ui: amazon-ebs: Do you want to continue? [Y/n] Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 hdf5-helpers amd64 1.8.16+docs-4ubuntu1 [12.5 kB]
amazon-ebs: Do you want to continue? [Y/n] Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 hdf5-helpers amd64 1.8.16+docs-4ubuntu1 [12.5 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec0 amd64 0.3.2-1 [18.0 kB]
amazon-ebs: Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec0 amd64 0.3.2-1 [18.0 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:3 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgfortran3 amd64 5.4.0-6ubuntu1~16.04.6 [260 kB]
amazon-ebs: Get:3 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgfortran3 amd64 5.4.0-6ubuntu1~16.04.6 [260 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:4 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libsz2 amd64 0.3.2-1 [5,048 B]
amazon-ebs: Get:4 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libsz2 amd64 0.3.2-1 [5,048 B]
2018/01/30 19:09:42 ui: amazon-ebs: Get:5 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-10 amd64 1.8.16+docs-4ubuntu1 [995 kB]
amazon-ebs: Get:5 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-10 amd64 1.8.16+docs-4ubuntu1 [995 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:6 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-cpp-11 amd64 1.8.16+docs-4ubuntu1 [101 kB]
amazon-ebs: Get:6 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-cpp-11 amd64 1.8.16+docs-4ubuntu1 [101 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:7 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg-turbo8-dev amd64 1.4.2-0ubuntu3 [254 kB]
amazon-ebs: Get:7 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg-turbo8-dev amd64 1.4.2-0ubuntu3 [254 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:8 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1,552 B]
amazon-ebs: Get:8 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1,552 B]
2018/01/30 19:09:42 ui: amazon-ebs: Get:9 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1,546 B]
amazon-ebs: Get:9 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1,546 B]
2018/01/30 19:09:42 ui: amazon-ebs: Get:10 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec-dev amd64 0.3.2-1 [16.6 kB]
amazon-ebs: Get:10 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec-dev amd64 0.3.2-1 [16.6 kB]
2018/01/30 19:09:42 ui: amazon-ebs: Get:11 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-dev amd64 1.8.16+docs-4ubuntu1 [5,005 kB]
amazon-ebs: Get:11 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-dev amd64 1.8.16+docs-4ubuntu1 [5,005 kB]
2018/01/30 19:09:42 ui: amazon-ebs: debconf: unable to initialize frontend: Dialog
amazon-ebs: debconf: unable to initialize frontend: Dialog
2018/01/30 19:09:42 ui: amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
2018/01/30 19:09:42 ui: amazon-ebs: debconf: falling back to frontend: Readline
amazon-ebs: debconf: falling back to frontend: Readline
2018/01/30 19:09:42 ui: amazon-ebs: debconf: unable to initialize frontend: Readline
amazon-ebs: debconf: unable to initialize frontend: Readline
2018/01/30 19:09:42 ui: amazon-ebs: debconf: (This frontend requires a controlling tty.)
amazon-ebs: debconf: (This frontend requires a controlling tty.)
2018/01/30 19:09:42 ui: amazon-ebs: debconf: falling back to frontend: Teletype
amazon-ebs: debconf: falling back to frontend: Teletype
2018/01/30 19:09:42 ui: amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
2018/01/30 19:09:42 ui: amazon-ebs: Fetched 6,670 kB in 0s (65.0 MB/s)
amazon-ebs: Fetched 6,670 kB in 0s (65.0 MB/s)
2018/01/30 19:09:42 ui: amazon-ebs: Selecting previously unselected package hdf5-helpers.
amazon-ebs: Selecting previously unselected package hdf5-helpers.
2018/01/30 19:09:42 ui: amazon-ebs: (Reading database ... 58369 files and directories currently installed.)
amazon-ebs: (Reading database ... 58369 files and directories currently installed.)
2018/01/30 19:09:42 ui: amazon-ebs: Preparing to unpack .../hdf5-helpers_1.8.16+docs-4ubuntu1_amd64.deb ...
amazon-ebs: Preparing to unpack .../hdf5-helpers_1.8.16+docs-4ubuntu1_amd64.deb ...
2018/01/30 19:09:42 ui: amazon-ebs: Unpacking hdf5-helpers (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Unpacking hdf5-helpers (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:42 ui: amazon-ebs: Selecting previously unselected package libaec0:amd64.
amazon-ebs: Selecting previously unselected package libaec0:amd64.
2018/01/30 19:09:42 ui: amazon-ebs: Preparing to unpack .../libaec0_0.3.2-1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libaec0_0.3.2-1_amd64.deb ...
2018/01/30 19:09:42 ui: amazon-ebs: Unpacking libaec0:amd64 (0.3.2-1) ...
amazon-ebs: Unpacking libaec0:amd64 (0.3.2-1) ...
2018/01/30 19:09:42 ui: amazon-ebs: Selecting previously unselected package libgfortran3:amd64.
amazon-ebs: Selecting previously unselected package libgfortran3:amd64.
2018/01/30 19:09:42 ui: amazon-ebs: Preparing to unpack .../libgfortran3_5.4.0-6ubuntu1~16.04.6_amd64.deb ...
amazon-ebs: Preparing to unpack .../libgfortran3_5.4.0-6ubuntu1~16.04.6_amd64.deb ...
2018/01/30 19:09:42 ui: amazon-ebs: Unpacking libgfortran3:amd64 (5.4.0-6ubuntu1~16.04.6) ...
amazon-ebs: Unpacking libgfortran3:amd64 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:42 ui: amazon-ebs: Selecting previously unselected package libsz2:amd64.
amazon-ebs: Selecting previously unselected package libsz2:amd64.
2018/01/30 19:09:42 ui: amazon-ebs: Preparing to unpack .../libsz2_0.3.2-1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libsz2_0.3.2-1_amd64.deb ...
2018/01/30 19:09:42 ui: amazon-ebs: Unpacking libsz2:amd64 (0.3.2-1) ...
amazon-ebs: Unpacking libsz2:amd64 (0.3.2-1) ...
2018/01/30 19:09:42 ui: amazon-ebs: Selecting previously unselected package libhdf5-10:amd64.
amazon-ebs: Selecting previously unselected package libhdf5-10:amd64.
2018/01/30 19:09:42 ui: amazon-ebs: Preparing to unpack .../libhdf5-10_1.8.16+docs-4ubuntu1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libhdf5-10_1.8.16+docs-4ubuntu1_amd64.deb ...
2018/01/30 19:09:42 ui: amazon-ebs: Unpacking libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Unpacking libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:43 ui: amazon-ebs: Selecting previously unselected package libhdf5-cpp-11:amd64.
amazon-ebs: Selecting previously unselected package libhdf5-cpp-11:amd64.
2018/01/30 19:09:43 ui: amazon-ebs: Preparing to unpack .../libhdf5-cpp-11_1.8.16+docs-4ubuntu1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libhdf5-cpp-11_1.8.16+docs-4ubuntu1_amd64.deb ...
2018/01/30 19:09:43 ui: amazon-ebs: Unpacking libhdf5-cpp-11:amd64 (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Unpacking libhdf5-cpp-11:amd64 (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:43 ui: amazon-ebs: Selecting previously unselected package libjpeg-turbo8-dev:amd64.
amazon-ebs: Selecting previously unselected package libjpeg-turbo8-dev:amd64.
2018/01/30 19:09:43 ui: amazon-ebs: Preparing to unpack .../libjpeg-turbo8-dev_1.4.2-0ubuntu3_amd64.deb ...
amazon-ebs: Preparing to unpack .../libjpeg-turbo8-dev_1.4.2-0ubuntu3_amd64.deb ...
2018/01/30 19:09:43 ui: amazon-ebs: Unpacking libjpeg-turbo8-dev:amd64 (1.4.2-0ubuntu3) ...
amazon-ebs: Unpacking libjpeg-turbo8-dev:amd64 (1.4.2-0ubuntu3) ...
2018/01/30 19:09:43 ui: amazon-ebs: Selecting previously unselected package libjpeg8-dev:amd64.
amazon-ebs: Selecting previously unselected package libjpeg8-dev:amd64.
2018/01/30 19:09:43 ui: amazon-ebs: Preparing to unpack .../libjpeg8-dev_8c-2ubuntu8_amd64.deb ...
amazon-ebs: Preparing to unpack .../libjpeg8-dev_8c-2ubuntu8_amd64.deb ...
2018/01/30 19:09:43 ui: amazon-ebs: Unpacking libjpeg8-dev:amd64 (8c-2ubuntu8) ...
amazon-ebs: Unpacking libjpeg8-dev:amd64 (8c-2ubuntu8) ...
2018/01/30 19:09:43 ui: amazon-ebs: Selecting previously unselected package libjpeg-dev:amd64.
amazon-ebs: Selecting previously unselected package libjpeg-dev:amd64.
2018/01/30 19:09:43 ui: amazon-ebs: Preparing to unpack .../libjpeg-dev_8c-2ubuntu8_amd64.deb ...
amazon-ebs: Preparing to unpack .../libjpeg-dev_8c-2ubuntu8_amd64.deb ...
2018/01/30 19:09:43 ui: amazon-ebs: Unpacking libjpeg-dev:amd64 (8c-2ubuntu8) ...
amazon-ebs: Unpacking libjpeg-dev:amd64 (8c-2ubuntu8) ...
2018/01/30 19:09:43 ui: amazon-ebs: Selecting previously unselected package libaec-dev:amd64.
amazon-ebs: Selecting previously unselected package libaec-dev:amd64.
2018/01/30 19:09:43 ui: amazon-ebs: Preparing to unpack .../libaec-dev_0.3.2-1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libaec-dev_0.3.2-1_amd64.deb ...
2018/01/30 19:09:43 ui: amazon-ebs: Unpacking libaec-dev:amd64 (0.3.2-1) ...
amazon-ebs: Unpacking libaec-dev:amd64 (0.3.2-1) ...
2018/01/30 19:09:43 ui: amazon-ebs: Selecting previously unselected package libhdf5-dev.
amazon-ebs: Selecting previously unselected package libhdf5-dev.
2018/01/30 19:09:43 ui: amazon-ebs: Preparing to unpack .../libhdf5-dev_1.8.16+docs-4ubuntu1_amd64.deb ...
amazon-ebs: Preparing to unpack .../libhdf5-dev_1.8.16+docs-4ubuntu1_amd64.deb ...
2018/01/30 19:09:43 ui: amazon-ebs: Unpacking libhdf5-dev (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Unpacking libhdf5-dev (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Processing triggers for libc-bin (2.23-0ubuntu10) ...
amazon-ebs: Processing triggers for libc-bin (2.23-0ubuntu10) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up hdf5-helpers (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Setting up hdf5-helpers (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libaec0:amd64 (0.3.2-1) ...
amazon-ebs: Setting up libaec0:amd64 (0.3.2-1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libgfortran3:amd64 (5.4.0-6ubuntu1~16.04.6) ...
amazon-ebs: Setting up libgfortran3:amd64 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libsz2:amd64 (0.3.2-1) ...
amazon-ebs: Setting up libsz2:amd64 (0.3.2-1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Setting up libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libhdf5-cpp-11:amd64 (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Setting up libhdf5-cpp-11:amd64 (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libjpeg-turbo8-dev:amd64 (1.4.2-0ubuntu3) ...
amazon-ebs: Setting up libjpeg-turbo8-dev:amd64 (1.4.2-0ubuntu3) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ...
amazon-ebs: Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ...
amazon-ebs: Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libaec-dev:amd64 (0.3.2-1) ...
amazon-ebs: Setting up libaec-dev:amd64 (0.3.2-1) ...
2018/01/30 19:09:44 ui: amazon-ebs: Setting up libhdf5-dev (1.8.16+docs-4ubuntu1) ...
amazon-ebs: Setting up libhdf5-dev (1.8.16+docs-4ubuntu1) ...
2018/01/30 19:09:44 ui: amazon-ebs: update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
amazon-ebs: update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
2018/01/30 19:09:44 ui: amazon-ebs: Processing triggers for libc-bin (2.23-0ubuntu10) ...
amazon-ebs: Processing triggers for libc-bin (2.23-0ubuntu10) ...
2018/01/30 19:09:45 ui: amazon-ebs: + yes
amazon-ebs: + yes
2018/01/30 19:09:45 ui: amazon-ebs: + sudo apt-get install 'libblas*'
amazon-ebs: + sudo apt-get install 'libblas*'
2018/01/30 19:09:45 ui: amazon-ebs: Reading package lists...
amazon-ebs: Reading package lists...
2018/01/30 19:09:45 ui: amazon-ebs: Building dependency tree...
amazon-ebs: Building dependency tree...
2018/01/30 19:09:45 ui: amazon-ebs: Reading state information...
amazon-ebs: Reading state information...
2018/01/30 19:09:45 ui: amazon-ebs: The following additional packages will be installed:
amazon-ebs: The following additional packages will be installed:
2018/01/30 19:09:45 ui: amazon-ebs: gfortran gfortran-5 libgfortran-5-dev liblapack-doc-man libpbdata libpbihdf
amazon-ebs: gfortran gfortran-5 libgfortran-5-dev liblapack-doc-man libpbdata libpbihdf
2018/01/30 19:09:45 ui: amazon-ebs: Suggested packages:
amazon-ebs: Suggested packages:
2018/01/30 19:09:45 ui: amazon-ebs: gfortran-multilib gfortran-doc gfortran-5-multilib gfortran-5-doc
amazon-ebs: gfortran-multilib gfortran-doc gfortran-5-multilib gfortran-5-doc
2018/01/30 19:09:45 ui: amazon-ebs: libgfortran3-dbg liblapack-doc
amazon-ebs: libgfortran3-dbg liblapack-doc
2018/01/30 19:09:45 ui: amazon-ebs: The following NEW packages will be installed:
amazon-ebs: The following NEW packages will be installed:
2018/01/30 19:09:45 ui: amazon-ebs: gfortran gfortran-5 libblas-common libblas-dev libblas-doc libblas-test
amazon-ebs: gfortran gfortran-5 libblas-common libblas-dev libblas-doc libblas-test
2018/01/30 19:09:45 ui: amazon-ebs: libblas3 libblasr libblasr-dev libgfortran-5-dev liblapack-doc-man libpbdata
amazon-ebs: libblas3 libblasr libblasr-dev libgfortran-5-dev liblapack-doc-man libpbdata
2018/01/30 19:09:45 ui: amazon-ebs: libpbihdf
amazon-ebs: libpbihdf
2018/01/30 19:09:45 ui: amazon-ebs: 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded.
amazon-ebs: 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded.
2018/01/30 19:09:45 ui: amazon-ebs: Need to get 16.2 MB of archives.
amazon-ebs: Need to get 16.2 MB of archives.
2018/01/30 19:09:45 ui: amazon-ebs: After this operation, 54.8 MB of additional disk space will be used.
amazon-ebs: After this operation, 54.8 MB of additional disk space will be used.
2018/01/30 19:09:45 ui: amazon-ebs: Do you want to continue? [Y/n] Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgfortran-5-dev amd64 5.4.0-6ubuntu1~16.04.6 [291 kB]
amazon-ebs: Do you want to continue? [Y/n] Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgfortran-5-dev amd64 5.4.0-6ubuntu1~16.04.6 [291 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 gfortran-5 amd64 5.4.0-6ubuntu1~16.04.6 [8,056 kB]
amazon-ebs: Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 gfortran-5 amd64 5.4.0-6ubuntu1~16.04.6 [8,056 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:3 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 gfortran amd64 4:5.3.1-1ubuntu1 [1,288 B]
amazon-ebs: Get:3 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 gfortran amd64 4:5.3.1-1ubuntu1 [1,288 B]
2018/01/30 19:09:45 ui: amazon-ebs: Get:4 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas-common amd64 3.6.0-2ubuntu2 [5,342 B]
amazon-ebs: Get:4 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas-common amd64 3.6.0-2ubuntu2 [5,342 B]
2018/01/30 19:09:45 ui: amazon-ebs: Get:5 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas3 amd64 3.6.0-2ubuntu2 [147 kB]
amazon-ebs: Get:5 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas3 amd64 3.6.0-2ubuntu2 [147 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:6 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas-dev amd64 3.6.0-2ubuntu2 [153 kB]
amazon-ebs: Get:6 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas-dev amd64 3.6.0-2ubuntu2 [153 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:7 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 liblapack-doc-man all 3.6.0-2ubuntu2 [4,552 kB]
amazon-ebs: Get:7 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 liblapack-doc-man all 3.6.0-2ubuntu2 [4,552 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:8 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas-doc all 3.6.0-2ubuntu2 [2,682 B]
amazon-ebs: Get:8 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libblas-doc all 3.6.0-2ubuntu2 [2,682 B]
2018/01/30 19:09:45 ui: amazon-ebs: Get:9 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libblas-test amd64 3.6.0-2ubuntu2 [304 kB]
amazon-ebs: Get:9 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libblas-test amd64 3.6.0-2ubuntu2 [304 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:10 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libpbdata amd64 0~20151014+gitbe5d1bf-2 [107 kB]
amazon-ebs: Get:10 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libpbdata amd64 0~20151014+gitbe5d1bf-2 [107 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:11 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libpbihdf amd64 0~20151014+gitbe5d1bf-2 [118 kB]
amazon-ebs: Get:11 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libpbihdf amd64 0~20151014+gitbe5d1bf-2 [118 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:12 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libblasr amd64 0~20151014+gitbe5d1bf-2 [809 kB]
amazon-ebs: Get:12 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libblasr amd64 0~20151014+gitbe5d1bf-2 [809 kB]
2018/01/30 19:09:45 ui: amazon-ebs: Get:13 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libblasr-dev amd64 0~20151014+gitbe5d1bf-2 [1,623 kB]
amazon-ebs: Get:13 http://us-west-2.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libblasr-dev amd64 0~20151014+gitbe5d1bf-2 [1,623 kB]
2018/01/30 19:09:45 ui: amazon-ebs: debconf: unable to initialize frontend: Dialog
amazon-ebs: debconf: unable to initialize frontend: Dialog
2018/01/30 19:09:45 ui: amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
amazon-ebs: debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
2018/01/30 19:09:45 ui: amazon-ebs: debconf: falling back to frontend: Readline
amazon-ebs: debconf: falling back to frontend: Readline
2018/01/30 19:09:45 ui: amazon-ebs: debconf: unable to initialize frontend: Readline
amazon-ebs: debconf: unable to initialize frontend: Readline
2018/01/30 19:09:45 ui: amazon-ebs: debconf: (This frontend requires a controlling tty.)
amazon-ebs: debconf: (This frontend requires a controlling tty.)
2018/01/30 19:09:45 ui: amazon-ebs: debconf: falling back to frontend: Teletype
amazon-ebs: debconf: falling back to frontend: Teletype
2018/01/30 19:09:45 ui: amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
amazon-ebs: dpkg-preconfigure: unable to re-open stdin:
2018/01/30 19:09:45 ui: amazon-ebs: Fetched 16.2 MB in 0s (35.3 MB/s)
amazon-ebs: Fetched 16.2 MB in 0s (35.3 MB/s)
2018/01/30 19:09:45 ui: amazon-ebs: Selecting previously unselected package libgfortran-5-dev:amd64.
amazon-ebs: Selecting previously unselected package libgfortran-5-dev:amd64.
2018/01/30 19:09:45 ui: amazon-ebs: (Reading database ... 58599 files and directories currently installed.)
amazon-ebs: (Reading database ... 58599 files and directories currently installed.)
2018/01/30 19:09:45 ui: amazon-ebs: Preparing to unpack .../libgfortran-5-dev_5.4.0-6ubuntu1~16.04.6_amd64.deb ...
amazon-ebs: Preparing to unpack .../libgfortran-5-dev_5.4.0-6ubuntu1~16.04.6_amd64.deb ...
2018/01/30 19:09:45 ui: amazon-ebs: Unpacking libgfortran-5-dev:amd64 (5.4.0-6ubuntu1~16.04.6) ...
amazon-ebs: Unpacking libgfortran-5-dev:amd64 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:46 ui: amazon-ebs: Selecting previously unselected package gfortran-5.
amazon-ebs: Selecting previously unselected package gfortran-5.
2018/01/30 19:09:46 ui: amazon-ebs: Preparing to unpack .../gfortran-5_5.4.0-6ubuntu1~16.04.6_amd64.deb ...
amazon-ebs: Preparing to unpack .../gfortran-5_5.4.0-6ubuntu1~16.04.6_amd64.deb ...
2018/01/30 19:09:46 ui: amazon-ebs: Unpacking gfortran-5 (5.4.0-6ubuntu1~16.04.6) ...
amazon-ebs: Unpacking gfortran-5 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:46 ui: amazon-ebs: Selecting previously unselected package gfortran.
amazon-ebs: Selecting previously unselected package gfortran.
2018/01/30 19:09:46 ui: amazon-ebs: Preparing to unpack .../gfortran_4%3a5.3.1-1ubuntu1_amd64.deb ...
amazon-ebs: Preparing to unpack .../gfortran_4%3a5.3.1-1ubuntu1_amd64.deb ...
2018/01/30 19:09:46 ui: amazon-ebs: Unpacking gfortran (4:5.3.1-1ubuntu1) ...
amazon-ebs: Unpacking gfortran (4:5.3.1-1ubuntu1) ...
2018/01/30 19:09:46 ui: amazon-ebs: Selecting previously unselected package libblas-common.
amazon-ebs: Selecting previously unselected package libblas-common.
2018/01/30 19:09:46 ui: amazon-ebs: Preparing to unpack .../libblas-common_3.6.0-2ubuntu2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libblas-common_3.6.0-2ubuntu2_amd64.deb ...
2018/01/30 19:09:46 ui: amazon-ebs: Unpacking libblas-common (3.6.0-2ubuntu2) ...
amazon-ebs: Unpacking libblas-common (3.6.0-2ubuntu2) ...
2018/01/30 19:09:46 ui: amazon-ebs: Selecting previously unselected package libblas3.
amazon-ebs: Selecting previously unselected package libblas3.
2018/01/30 19:09:46 ui: amazon-ebs: Preparing to unpack .../libblas3_3.6.0-2ubuntu2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libblas3_3.6.0-2ubuntu2_amd64.deb ...
2018/01/30 19:09:46 ui: amazon-ebs: Unpacking libblas3 (3.6.0-2ubuntu2) ...
amazon-ebs: Unpacking libblas3 (3.6.0-2ubuntu2) ...
2018/01/30 19:09:47 ui: amazon-ebs: Selecting previously unselected package libblas-dev.
amazon-ebs: Selecting previously unselected package libblas-dev.
2018/01/30 19:09:47 ui: amazon-ebs: Preparing to unpack .../libblas-dev_3.6.0-2ubuntu2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libblas-dev_3.6.0-2ubuntu2_amd64.deb ...
2018/01/30 19:09:47 ui: amazon-ebs: Unpacking libblas-dev (3.6.0-2ubuntu2) ...
amazon-ebs: Unpacking libblas-dev (3.6.0-2ubuntu2) ...
2018/01/30 19:09:47 ui: amazon-ebs: Selecting previously unselected package liblapack-doc-man.
amazon-ebs: Selecting previously unselected package liblapack-doc-man.
2018/01/30 19:09:47 ui: amazon-ebs: Preparing to unpack .../liblapack-doc-man_3.6.0-2ubuntu2_all.deb ...
amazon-ebs: Preparing to unpack .../liblapack-doc-man_3.6.0-2ubuntu2_all.deb ...
2018/01/30 19:09:47 ui: amazon-ebs: Unpacking liblapack-doc-man (3.6.0-2ubuntu2) ...
amazon-ebs: Unpacking liblapack-doc-man (3.6.0-2ubuntu2) ...
2018/01/30 19:09:48 ui: amazon-ebs: Selecting previously unselected package libblas-doc.
amazon-ebs: Selecting previously unselected package libblas-doc.
2018/01/30 19:09:48 ui: amazon-ebs: Preparing to unpack .../libblas-doc_3.6.0-2ubuntu2_all.deb ...
amazon-ebs: Preparing to unpack .../libblas-doc_3.6.0-2ubuntu2_all.deb ...
2018/01/30 19:09:48 ui: amazon-ebs: Unpacking libblas-doc (3.6.0-2ubuntu2) ...
amazon-ebs: Unpacking libblas-doc (3.6.0-2ubuntu2) ...
2018/01/30 19:09:48 ui: amazon-ebs: Selecting previously unselected package libblas-test.
amazon-ebs: Selecting previously unselected package libblas-test.
2018/01/30 19:09:48 ui: amazon-ebs: Preparing to unpack .../libblas-test_3.6.0-2ubuntu2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libblas-test_3.6.0-2ubuntu2_amd64.deb ...
2018/01/30 19:09:48 ui: amazon-ebs: Unpacking libblas-test (3.6.0-2ubuntu2) ...
amazon-ebs: Unpacking libblas-test (3.6.0-2ubuntu2) ...
2018/01/30 19:09:48 ui: amazon-ebs: Selecting previously unselected package libpbdata:amd64.
amazon-ebs: Selecting previously unselected package libpbdata:amd64.
2018/01/30 19:09:48 ui: amazon-ebs: Preparing to unpack .../libpbdata_0~20151014+gitbe5d1bf-2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libpbdata_0~20151014+gitbe5d1bf-2_amd64.deb ...
2018/01/30 19:09:48 ui: amazon-ebs: Unpacking libpbdata:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Unpacking libpbdata:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:48 ui: amazon-ebs: Selecting previously unselected package libpbihdf:amd64.
amazon-ebs: Selecting previously unselected package libpbihdf:amd64.
2018/01/30 19:09:48 ui: amazon-ebs: Preparing to unpack .../libpbihdf_0~20151014+gitbe5d1bf-2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libpbihdf_0~20151014+gitbe5d1bf-2_amd64.deb ...
2018/01/30 19:09:48 ui: amazon-ebs: Unpacking libpbihdf:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Unpacking libpbihdf:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:48 ui: amazon-ebs: Selecting previously unselected package libblasr:amd64.
amazon-ebs: Selecting previously unselected package libblasr:amd64.
2018/01/30 19:09:48 ui: amazon-ebs: Preparing to unpack .../libblasr_0~20151014+gitbe5d1bf-2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libblasr_0~20151014+gitbe5d1bf-2_amd64.deb ...
2018/01/30 19:09:48 ui: amazon-ebs: Unpacking libblasr:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Unpacking libblasr:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:49 ui: amazon-ebs: Selecting previously unselected package libblasr-dev:amd64.
amazon-ebs: Selecting previously unselected package libblasr-dev:amd64.
2018/01/30 19:09:49 ui: amazon-ebs: Preparing to unpack .../libblasr-dev_0~20151014+gitbe5d1bf-2_amd64.deb ...
amazon-ebs: Preparing to unpack .../libblasr-dev_0~20151014+gitbe5d1bf-2_amd64.deb ...
2018/01/30 19:09:49 ui: amazon-ebs: Unpacking libblasr-dev:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Unpacking libblasr-dev:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:49 ui: amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
amazon-ebs: Processing triggers for man-db (2.7.5-1) ...
amazon-ebs: Setting up libgfortran-5-dev:amd64 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:57 ui: amazon-ebs: Setting up libgfortran-5-dev:amd64 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:57 ui: amazon-ebs: Setting up gfortran-5 (5.4.0-6ubuntu1~16.04.6) ...
amazon-ebs: Setting up gfortran-5 (5.4.0-6ubuntu1~16.04.6) ...
2018/01/30 19:09:57 ui: amazon-ebs: Setting up gfortran (4:5.3.1-1ubuntu1) ...
amazon-ebs: Setting up gfortran (4:5.3.1-1ubuntu1) ...
2018/01/30 19:09:57 ui: amazon-ebs: update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
amazon-ebs: update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
2018/01/30 19:09:58 ui: amazon-ebs: update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
amazon-ebs: update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblas-common (3.6.0-2ubuntu2) ...
amazon-ebs: Setting up libblas-common (3.6.0-2ubuntu2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblas3 (3.6.0-2ubuntu2) ...
amazon-ebs: Setting up libblas3 (3.6.0-2ubuntu2) ...
2018/01/30 19:09:58 ui: amazon-ebs: update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
amazon-ebs: update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblas-dev (3.6.0-2ubuntu2) ...
amazon-ebs: Setting up libblas-dev (3.6.0-2ubuntu2) ...
2018/01/30 19:09:58 ui: amazon-ebs: update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
amazon-ebs: update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
2018/01/30 19:09:58 ui: amazon-ebs: Setting up liblapack-doc-man (3.6.0-2ubuntu2) ...
amazon-ebs: Setting up liblapack-doc-man (3.6.0-2ubuntu2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblas-doc (3.6.0-2ubuntu2) ...
amazon-ebs: Setting up libblas-doc (3.6.0-2ubuntu2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblas-test (3.6.0-2ubuntu2) ...
amazon-ebs: Setting up libblas-test (3.6.0-2ubuntu2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libpbdata:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Setting up libpbdata:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libpbihdf:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Setting up libpbihdf:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblasr:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Setting up libblasr:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:58 ui: amazon-ebs: Setting up libblasr-dev:amd64 (0~20151014+gitbe5d1bf-2) ...
amazon-ebs: Setting up libblasr-dev:amd64 (0~20151014+gitbe5d1bf-2) ...
2018/01/30 19:09:58 ui: amazon-ebs: + yes
amazon-ebs: + yes
2018/01/30 19:09:58 ui: amazon-ebs: + sudo apt-get clean
amazon-ebs: + sudo apt-get clean
2018/01/30 19:09:58 ui: amazon-ebs: + yes
amazon-ebs: + yes
2018/01/30 19:09:58 ui: amazon-ebs: + conda clean --tarballs
amazon-ebs: + conda clean --tarballs
2018/01/30 19:09:59 ui: amazon-ebs: Cache location: /home/ubuntu/anaconda/pkgs
amazon-ebs: Cache location: /home/ubuntu/anaconda/pkgs
2018/01/30 19:09:59 ui: amazon-ebs: Will remove the following tarballs:
amazon-ebs: Will remove the following tarballs:
amazon-ebs:
2018/01/30 19:09:59 ui: amazon-ebs:
2018/01/30 19:09:59 ui: amazon-ebs: /home/ubuntu/anaconda/pkgs
amazon-ebs: /home/ubuntu/anaconda/pkgs
2018/01/30 19:09:59 ui: amazon-ebs: --------------------------
amazon-ebs: --------------------------
2018/01/30 19:09:59 ui: amazon-ebs: chardet-3.0.4-py36h0f667ec_1.tar.bz2 190 KB
amazon-ebs: chardet-3.0.4-py36h0f667ec_1.tar.bz2 190 KB
2018/01/30 19:09:59 ui: amazon-ebs: conda-env-2.6.0-0.tar.bz2 1017 B
amazon-ebs: conda-env-2.6.0-0.tar.bz2 1017 B
2018/01/30 19:09:59 ui: amazon-ebs: libgcc-ng-7.2.0-h7cc24e2_2.tar.bz2 6.1 MB
amazon-ebs: libgcc-ng-7.2.0-h7cc24e2_2.tar.bz2 6.1 MB
2018/01/30 19:09:59 ui: amazon-ebs: libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2 2.5 MB
amazon-ebs: libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2 2.5 MB
2018/01/30 19:09:59 ui: amazon-ebs: pip-9.0.1-py36h6c6f9ce_4.tar.bz2 2.2 MB
amazon-ebs: pip-9.0.1-py36h6c6f9ce_4.tar.bz2 2.2 MB
2018/01/30 19:09:59 ui: amazon-ebs: biopython-1.70-np112py36_1.tar.bz2 2.6 MB
amazon-ebs: biopython-1.70-np112py36_1.tar.bz2 2.6 MB
2018/01/30 19:09:59 ui: amazon-ebs: mmtf-python-1.0.10-py_0.tar.bz2 22 KB
amazon-ebs: mmtf-python-1.0.10-py_0.tar.bz2 22 KB
2018/01/30 19:09:59 ui: amazon-ebs: asn1crypto-0.23.0-py36h4639342_0.tar.bz2 151 KB
amazon-ebs: asn1crypto-0.23.0-py36h4639342_0.tar.bz2 151 KB
2018/01/30 19:09:59 ui: amazon-ebs: certifi-2017.11.5-py36_0.tar.bz2 195 KB
amazon-ebs: certifi-2017.11.5-py36_0.tar.bz2 195 KB
2018/01/30 19:09:59 ui: amazon-ebs: conda-4.3.31-py36_0.tar.bz2 513 KB
amazon-ebs: conda-4.3.31-py36_0.tar.bz2 513 KB
2018/01/30 19:09:59 ui: amazon-ebs: sqlite-3.20.1-hb898158_2.tar.bz2 1.5 MB
amazon-ebs: sqlite-3.20.1-hb898158_2.tar.bz2 1.5 MB
2018/01/30 19:09:59 ui: amazon-ebs: ca-certificates-2017.08.26-h1d4fec5_0.tar.bz2 263 KB
amazon-ebs: ca-certificates-2017.08.26-h1d4fec5_0.tar.bz2 263 KB
2018/01/30 19:09:59 ui: amazon-ebs: zlib-1.2.11-ha838bed_2.tar.bz2 101 KB
amazon-ebs: zlib-1.2.11-ha838bed_2.tar.bz2 101 KB
2018/01/30 19:09:59 ui: amazon-ebs: readline-7.0-ha6073c6_4.tar.bz2 1.1 MB
amazon-ebs: readline-7.0-ha6073c6_4.tar.bz2 1.1 MB
2018/01/30 19:09:59 ui: amazon-ebs: tk-8.6.7-hc745277_3.tar.bz2 3.2 MB
amazon-ebs: tk-8.6.7-hc745277_3.tar.bz2 3.2 MB
2018/01/30 19:09:59 ui: amazon-ebs: pip-9.0.1-py36_1.tar.bz2 1.7 MB
amazon-ebs: pip-9.0.1-py36_1.tar.bz2 1.7 MB
2018/01/30 19:09:59 ui: amazon-ebs: python-3.6.3-h6c0c0dc_5.tar.bz2 29.0 MB
amazon-ebs: python-3.6.3-h6c0c0dc_5.tar.bz2 29.0 MB
2018/01/30 19:09:59 ui: amazon-ebs: six-1.11.0-py36h372c433_1.tar.bz2 21 KB
amazon-ebs: six-1.11.0-py36h372c433_1.tar.bz2 21 KB
2018/01/30 19:09:59 ui: amazon-ebs: idna-2.6-py36h82fb2a8_1.tar.bz2 122 KB
amazon-ebs: idna-2.6-py36h82fb2a8_1.tar.bz2 122 KB
2018/01/30 19:09:59 ui: amazon-ebs: intel-openmp-2018.0.0-hc7b2577_8.tar.bz2 618 KB
amazon-ebs: intel-openmp-2018.0.0-hc7b2577_8.tar.bz2 618 KB
2018/01/30 19:09:59 ui: amazon-ebs: jpeg-9b-2.tar.bz2 1.0 MB
amazon-ebs: jpeg-9b-2.tar.bz2 1.0 MB
2018/01/30 19:09:59 ui: amazon-ebs: xz-5.2.3-h55aa19d_2.tar.bz2 357 KB
amazon-ebs: xz-5.2.3-h55aa19d_2.tar.bz2 357 KB
2018/01/30 19:09:59 ui: amazon-ebs: readline-7.0-0.tar.bz2 838 KB
amazon-ebs: readline-7.0-0.tar.bz2 838 KB
2018/01/30 19:09:59 ui: amazon-ebs: conda-4.4.8-py36_0.tar.bz2 932 KB
amazon-ebs: conda-4.4.8-py36_0.tar.bz2 932 KB
2018/01/30 19:09:59 ui: amazon-ebs: cryptography-2.1.4-py36hd09be54_0.tar.bz2 600 KB
amazon-ebs: cryptography-2.1.4-py36hd09be54_0.tar.bz2 600 KB
2018/01/30 19:09:59 ui: amazon-ebs: ruamel_yaml-0.11.14-py36ha2fb22d_2.tar.bz2 210 KB
amazon-ebs: ruamel_yaml-0.11.14-py36ha2fb22d_2.tar.bz2 210 KB
2018/01/30 19:09:59 ui: amazon-ebs: setuptools-38.4.0-py36_0.tar.bz2 524 KB
amazon-ebs: setuptools-38.4.0-py36_0.tar.bz2 524 KB
2018/01/30 19:09:59 ui: amazon-ebs: conda-4.3.33-py36_0.tar.bz2 514 KB
amazon-ebs: conda-4.3.33-py36_0.tar.bz2 514 KB
2018/01/30 19:09:59 ui: amazon-ebs: freetype-2.7-1.tar.bz2 2.8 MB
amazon-ebs: freetype-2.7-1.tar.bz2 2.8 MB
2018/01/30 19:09:59 ui: amazon-ebs: xz-5.2.3-0.tar.bz2 854 KB
amazon-ebs: xz-5.2.3-0.tar.bz2 854 KB
2018/01/30 19:09:59 ui: amazon-ebs: libffi-3.2.1-hd88cf55_4.tar.bz2 43 KB
amazon-ebs: libffi-3.2.1-hd88cf55_4.tar.bz2 43 KB
2018/01/30 19:09:59 ui: amazon-ebs: zlib-1.2.11-0.tar.bz2 93 KB
amazon-ebs: zlib-1.2.11-0.tar.bz2 93 KB
2018/01/30 19:09:59 ui: amazon-ebs: urllib3-1.22-py36hbe7ace6_0.tar.bz2 155 KB
amazon-ebs: urllib3-1.22-py36hbe7ace6_0.tar.bz2 155 KB
2018/01/30 19:09:59 ui: amazon-ebs: numpy-1.12.1-py36he24570b_1.tar.bz2 3.8 MB
amazon-ebs: numpy-1.12.1-py36he24570b_1.tar.bz2 3.8 MB
2018/01/30 19:09:59 ui: amazon-ebs: ncurses-5.9-10.tar.bz2 1.1 MB
amazon-ebs: ncurses-5.9-10.tar.bz2 1.1 MB
2018/01/30 19:09:59 ui: amazon-ebs: pyopenssl-17.5.0-py36h20ba746_0.tar.bz2 79 KB
amazon-ebs: pyopenssl-17.5.0-py36h20ba746_0.tar.bz2 79 KB
2018/01/30 19:09:59 ui: amazon-ebs: reportlab-3.4.0-py36_0.tar.bz2 2.4 MB
amazon-ebs: reportlab-3.4.0-py36_0.tar.bz2 2.4 MB
2018/01/30 19:09:59 ui: amazon-ebs: wheel-0.30.0-py36_2.tar.bz2 66 KB
amazon-ebs: wheel-0.30.0-py36_2.tar.bz2 66 KB
2018/01/30 19:09:59 ui: amazon-ebs: ncurses-6.0-h9df7e31_2.tar.bz2 920 KB
amazon-ebs: ncurses-6.0-h9df7e31_2.tar.bz2 920 KB
2018/01/30 19:09:59 ui: amazon-ebs: openssl-1.0.2n-0.tar.bz2 3.5 MB
amazon-ebs: openssl-1.0.2n-0.tar.bz2 3.5 MB
2018/01/30 19:09:59 ui: amazon-ebs: certifi-2017.11.5-py36hf29ccca_0.tar.bz2 196 KB
amazon-ebs: certifi-2017.11.5-py36hf29ccca_0.tar.bz2 196 KB
2018/01/30 19:09:59 ui: amazon-ebs: cffi-1.11.2-py36h2825082_0.tar.bz2 212 KB
amazon-ebs: cffi-1.11.2-py36h2825082_0.tar.bz2 212 KB
2018/01/30 19:09:59 ui: amazon-ebs: yaml-0.1.7-had09818_2.tar.bz2 85 KB
amazon-ebs: yaml-0.1.7-had09818_2.tar.bz2 85 KB
2018/01/30 19:09:59 ui: amazon-ebs: libpng-1.6.34-0.tar.bz2 305 KB
amazon-ebs: libpng-1.6.34-0.tar.bz2 305 KB
2018/01/30 19:09:59 ui: amazon-ebs: _license-1.1-py36_1.tar.bz2 356 KB
amazon-ebs: _license-1.1-py36_1.tar.bz2 356 KB
2018/01/30 19:09:59 ui: amazon-ebs: mkl-2018.0.1-h19d6760_4.tar.bz2 184.7 MB
amazon-ebs: mkl-2018.0.1-h19d6760_4.tar.bz2 184.7 MB
2018/01/30 19:09:59 ui: amazon-ebs: olefile-0.44-py36_0.tar.bz2 51 KB
amazon-ebs: olefile-0.44-py36_0.tar.bz2 51 KB
2018/01/30 19:09:59 ui: amazon-ebs: virtualenv-15.1.0-py36_0.tar.bz2 1.8 MB
amazon-ebs: virtualenv-15.1.0-py36_0.tar.bz2 1.8 MB
2018/01/30 19:09:59 ui: amazon-ebs: sqlite-3.20.1-2.tar.bz2 1.3 MB
amazon-ebs: sqlite-3.20.1-2.tar.bz2 1.3 MB
2018/01/30 19:09:59 ui: amazon-ebs: pysocks-1.6.7-py36hd97a5b1_1.tar.bz2 22 KB
amazon-ebs: pysocks-1.6.7-py36hd97a5b1_1.tar.bz2 22 KB
2018/01/30 19:09:59 ui: amazon-ebs: requests-2.18.4-py36he2e5f8d_1.tar.bz2 92 KB
amazon-ebs: requests-2.18.4-py36he2e5f8d_1.tar.bz2 92 KB
2018/01/30 19:09:59 ui: amazon-ebs: conda-env-2.6.0-h36134e3_1.tar.bz2 2 KB
amazon-ebs: conda-env-2.6.0-h36134e3_1.tar.bz2 2 KB
2018/01/30 19:09:59 ui: amazon-ebs: openssl-1.0.2n-hb7f436b_0.tar.bz2 3.4 MB
amazon-ebs: openssl-1.0.2n-hb7f436b_0.tar.bz2 3.4 MB
2018/01/30 19:09:59 ui: amazon-ebs: libtiff-4.0.9-0.tar.bz2 511 KB
amazon-ebs: libtiff-4.0.9-0.tar.bz2 511 KB
2018/01/30 19:09:59 ui: amazon-ebs: libedit-3.1-heed3624_0.tar.bz2 171 KB
amazon-ebs: libedit-3.1-heed3624_0.tar.bz2 171 KB
2018/01/30 19:09:59 ui: amazon-ebs: + df -h
amazon-ebs: + df -h
2018/01/30 19:09:59 ui: amazon-ebs: ca-certificates-2017.11.5-0.tar.bz2 145 KB
amazon-ebs: ca-certificates-2017.11.5-0.tar.bz2 145 KB
2018/01/30 19:09:59 ui: amazon-ebs: + echo 'setting up pomoxis'
amazon-ebs: + echo 'setting up pomoxis'
2018/01/30 19:09:59 ui: amazon-ebs: pillow-4.2.1-py36_0.tar.bz2 933 KB
amazon-ebs: pillow-4.2.1-py36_0.tar.bz2 933 KB
2018/01/30 19:09:59 ui: amazon-ebs: + git clone --recursive https://github.com/nanoporetech/pomoxis
amazon-ebs: + git clone --recursive https://github.com/nanoporetech/pomoxis
2018/01/30 19:09:59 ui: amazon-ebs: python-3.6.4-0.tar.bz2 19.1 MB
amazon-ebs: python-3.6.4-0.tar.bz2 19.1 MB
2018/01/30 19:09:59 ui: amazon-ebs: wheel-0.30.0-py36hfd4bba0_1.tar.bz2 67 KB
amazon-ebs: wheel-0.30.0-py36hfd4bba0_1.tar.bz2 67 KB
2018/01/30 19:09:59 ui: amazon-ebs: pycparser-2.18-py36hf9f622e_1.tar.bz2 169 KB
amazon-ebs: pycparser-2.18-py36hf9f622e_1.tar.bz2 169 KB
2018/01/30 19:09:59 ui: amazon-ebs: setuptools-36.5.0-py36he42e2e1_0.tar.bz2 512 KB
amazon-ebs: setuptools-36.5.0-py36he42e2e1_0.tar.bz2 512 KB
2018/01/30 19:09:59 ui: amazon-ebs: pycosat-0.6.3-py36h0a5515d_0.tar.bz2 104 KB
amazon-ebs: pycosat-0.6.3-py36h0a5515d_0.tar.bz2 104 KB
2018/01/30 19:09:59 ui: amazon-ebs: msgpack-python-0.5.1-py36_0.tar.bz2 312 KB
amazon-ebs: msgpack-python-0.5.1-py36_0.tar.bz2 312 KB
2018/01/30 19:09:59 ui: amazon-ebs: tk-8.6.7-0.tar.bz2 3.1 MB
amazon-ebs: tk-8.6.7-0.tar.bz2 3.1 MB
2018/01/30 19:09:59 ui: amazon-ebs: libgfortran-ng-7.2.0-h9f7466a_2.tar.bz2 349 KB
amazon-ebs: libgfortran-ng-7.2.0-h9f7466a_2.tar.bz2 349 KB
2018/01/30 19:09:59 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:59 ui: amazon-ebs: ---------------------------------------------------
amazon-ebs: ---------------------------------------------------
2018/01/30 19:09:59 ui: amazon-ebs: Total: 290.4 MB
amazon-ebs: Total: 290.4 MB
2018/01/30 19:09:59 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:09:59 ui: amazon-ebs: Removed chardet-3.0.4-py36h0f667ec_1.tar.bz2
amazon-ebs: Removed chardet-3.0.4-py36h0f667ec_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed conda-env-2.6.0-0.tar.bz2
amazon-ebs: Removed conda-env-2.6.0-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libgcc-ng-7.2.0-h7cc24e2_2.tar.bz2
amazon-ebs: Removed libgcc-ng-7.2.0-h7cc24e2_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2
amazon-ebs: Removed libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pip-9.0.1-py36h6c6f9ce_4.tar.bz2
amazon-ebs: Removed pip-9.0.1-py36h6c6f9ce_4.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed biopython-1.70-np112py36_1.tar.bz2
amazon-ebs: Removed biopython-1.70-np112py36_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed mmtf-python-1.0.10-py_0.tar.bz2
amazon-ebs: Removed mmtf-python-1.0.10-py_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed asn1crypto-0.23.0-py36h4639342_0.tar.bz2
amazon-ebs: Removed asn1crypto-0.23.0-py36h4639342_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed certifi-2017.11.5-py36_0.tar.bz2
amazon-ebs: Removed certifi-2017.11.5-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed conda-4.3.31-py36_0.tar.bz2
amazon-ebs: Removed conda-4.3.31-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed sqlite-3.20.1-hb898158_2.tar.bz2
amazon-ebs: Removed sqlite-3.20.1-hb898158_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed ca-certificates-2017.08.26-h1d4fec5_0.tar.bz2
amazon-ebs: Removed ca-certificates-2017.08.26-h1d4fec5_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed zlib-1.2.11-ha838bed_2.tar.bz2
amazon-ebs: Removed zlib-1.2.11-ha838bed_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed readline-7.0-ha6073c6_4.tar.bz2
amazon-ebs: Removed readline-7.0-ha6073c6_4.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed tk-8.6.7-hc745277_3.tar.bz2
amazon-ebs: Removed tk-8.6.7-hc745277_3.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pip-9.0.1-py36_1.tar.bz2
amazon-ebs: Removed pip-9.0.1-py36_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed python-3.6.3-h6c0c0dc_5.tar.bz2
amazon-ebs: Removed python-3.6.3-h6c0c0dc_5.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed six-1.11.0-py36h372c433_1.tar.bz2
amazon-ebs: Removed six-1.11.0-py36h372c433_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed idna-2.6-py36h82fb2a8_1.tar.bz2
amazon-ebs: Removed idna-2.6-py36h82fb2a8_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed intel-openmp-2018.0.0-hc7b2577_8.tar.bz2
amazon-ebs: Removed intel-openmp-2018.0.0-hc7b2577_8.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed jpeg-9b-2.tar.bz2
amazon-ebs: Removed jpeg-9b-2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed xz-5.2.3-h55aa19d_2.tar.bz2
amazon-ebs: Removed xz-5.2.3-h55aa19d_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed readline-7.0-0.tar.bz2
amazon-ebs: Removed readline-7.0-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed conda-4.4.8-py36_0.tar.bz2
amazon-ebs: Removed conda-4.4.8-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed cryptography-2.1.4-py36hd09be54_0.tar.bz2
amazon-ebs: Removed cryptography-2.1.4-py36hd09be54_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed ruamel_yaml-0.11.14-py36ha2fb22d_2.tar.bz2
amazon-ebs: Removed ruamel_yaml-0.11.14-py36ha2fb22d_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed setuptools-38.4.0-py36_0.tar.bz2
amazon-ebs: Removed setuptools-38.4.0-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed conda-4.3.33-py36_0.tar.bz2
amazon-ebs: Removed conda-4.3.33-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed freetype-2.7-1.tar.bz2
amazon-ebs: Removed freetype-2.7-1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed xz-5.2.3-0.tar.bz2
amazon-ebs: Removed xz-5.2.3-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libffi-3.2.1-hd88cf55_4.tar.bz2
amazon-ebs: Removed libffi-3.2.1-hd88cf55_4.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed zlib-1.2.11-0.tar.bz2
amazon-ebs: Removed zlib-1.2.11-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed urllib3-1.22-py36hbe7ace6_0.tar.bz2
amazon-ebs: Removed urllib3-1.22-py36hbe7ace6_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Cloning into 'pomoxis'...
amazon-ebs: Cloning into 'pomoxis'...
2018/01/30 19:09:59 ui: amazon-ebs: Removed numpy-1.12.1-py36he24570b_1.tar.bz2
amazon-ebs: Removed numpy-1.12.1-py36he24570b_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed ncurses-5.9-10.tar.bz2
amazon-ebs: Removed ncurses-5.9-10.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pyopenssl-17.5.0-py36h20ba746_0.tar.bz2
amazon-ebs: Removed pyopenssl-17.5.0-py36h20ba746_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed reportlab-3.4.0-py36_0.tar.bz2
amazon-ebs: Removed reportlab-3.4.0-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed wheel-0.30.0-py36_2.tar.bz2
amazon-ebs: Removed wheel-0.30.0-py36_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed ncurses-6.0-h9df7e31_2.tar.bz2
amazon-ebs: Removed ncurses-6.0-h9df7e31_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed openssl-1.0.2n-0.tar.bz2
amazon-ebs: Removed openssl-1.0.2n-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed certifi-2017.11.5-py36hf29ccca_0.tar.bz2
amazon-ebs: Removed certifi-2017.11.5-py36hf29ccca_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed cffi-1.11.2-py36h2825082_0.tar.bz2
amazon-ebs: Removed cffi-1.11.2-py36h2825082_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed yaml-0.1.7-had09818_2.tar.bz2
amazon-ebs: Removed yaml-0.1.7-had09818_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libpng-1.6.34-0.tar.bz2
amazon-ebs: Removed libpng-1.6.34-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed _license-1.1-py36_1.tar.bz2
amazon-ebs: Removed _license-1.1-py36_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed mkl-2018.0.1-h19d6760_4.tar.bz2
amazon-ebs: Removed mkl-2018.0.1-h19d6760_4.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed olefile-0.44-py36_0.tar.bz2
amazon-ebs: Removed olefile-0.44-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed virtualenv-15.1.0-py36_0.tar.bz2
amazon-ebs: Removed virtualenv-15.1.0-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed sqlite-3.20.1-2.tar.bz2
amazon-ebs: Removed sqlite-3.20.1-2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pysocks-1.6.7-py36hd97a5b1_1.tar.bz2
amazon-ebs: Removed pysocks-1.6.7-py36hd97a5b1_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed requests-2.18.4-py36he2e5f8d_1.tar.bz2
amazon-ebs: Removed requests-2.18.4-py36he2e5f8d_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed conda-env-2.6.0-h36134e3_1.tar.bz2
amazon-ebs: Removed conda-env-2.6.0-h36134e3_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed openssl-1.0.2n-hb7f436b_0.tar.bz2
amazon-ebs: Removed openssl-1.0.2n-hb7f436b_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libtiff-4.0.9-0.tar.bz2
amazon-ebs: Removed libtiff-4.0.9-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libedit-3.1-heed3624_0.tar.bz2
amazon-ebs: Removed libedit-3.1-heed3624_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed ca-certificates-2017.11.5-0.tar.bz2
amazon-ebs: Removed ca-certificates-2017.11.5-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pillow-4.2.1-py36_0.tar.bz2
amazon-ebs: Removed pillow-4.2.1-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed python-3.6.4-0.tar.bz2
amazon-ebs: Removed python-3.6.4-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed wheel-0.30.0-py36hfd4bba0_1.tar.bz2
amazon-ebs: Removed wheel-0.30.0-py36hfd4bba0_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pycparser-2.18-py36hf9f622e_1.tar.bz2
amazon-ebs: Removed pycparser-2.18-py36hf9f622e_1.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed setuptools-36.5.0-py36he42e2e1_0.tar.bz2
amazon-ebs: Removed setuptools-36.5.0-py36he42e2e1_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed pycosat-0.6.3-py36h0a5515d_0.tar.bz2
amazon-ebs: Removed pycosat-0.6.3-py36h0a5515d_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed msgpack-python-0.5.1-py36_0.tar.bz2
amazon-ebs: Removed msgpack-python-0.5.1-py36_0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed tk-8.6.7-0.tar.bz2
amazon-ebs: Removed tk-8.6.7-0.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Removed libgfortran-ng-7.2.0-h9f7466a_2.tar.bz2
amazon-ebs: Removed libgfortran-ng-7.2.0-h9f7466a_2.tar.bz2
2018/01/30 19:09:59 ui: amazon-ebs: Filesystem Size Used Avail Use% Mounted on
amazon-ebs: Filesystem Size Used Avail Use% Mounted on
2018/01/30 19:09:59 ui: amazon-ebs: udev 32G 0 32G 0% /dev
amazon-ebs: udev 32G 0 32G 0% /dev
2018/01/30 19:09:59 ui: amazon-ebs: tmpfs 6.3G 8.6M 6.3G 1% /run
amazon-ebs: tmpfs 6.3G 8.6M 6.3G 1% /run
2018/01/30 19:09:59 ui: amazon-ebs: /dev/xvda1 7.7G 2.6G 5.1G 34% /
amazon-ebs: /dev/xvda1 7.7G 2.6G 5.1G 34% /
2018/01/30 19:09:59 ui: amazon-ebs: tmpfs 32G 0 32G 0% /dev/shm
amazon-ebs: tmpfs 32G 0 32G 0% /dev/shm
2018/01/30 19:09:59 ui: amazon-ebs: tmpfs 5.0M 0 5.0M 0% /run/lock
amazon-ebs: tmpfs 5.0M 0 5.0M 0% /run/lock
2018/01/30 19:09:59 ui: amazon-ebs: tmpfs 32G 0 32G 0% /sys/fs/cgroup
amazon-ebs: tmpfs 32G 0 32G 0% /sys/fs/cgroup
2018/01/30 19:09:59 ui: amazon-ebs: tmpfs 6.3G 0 6.3G 0% /run/user/1000
amazon-ebs: tmpfs 6.3G 0 6.3G 0% /run/user/1000
2018/01/30 19:09:59 ui: amazon-ebs: setting up pomoxis
amazon-ebs: setting up pomoxis
2018/01/30 19:09:59 ui: amazon-ebs: Submodule 'submodules/bwa' (https://github.com/lh3/bwa) registered for path 'submodules/bwa'
amazon-ebs: Submodule 'submodules/bwa' (https://github.com/lh3/bwa) registered for path 'submodules/bwa'
2018/01/30 19:09:59 ui: amazon-ebs: Submodule 'submodules/miniasm' (https://github.com/lh3/miniasm) registered for path 'submodules/miniasm'
amazon-ebs: Submodule 'submodules/miniasm' (https://github.com/lh3/miniasm) registered for path 'submodules/miniasm'
2018/01/30 19:09:59 ui: amazon-ebs: Submodule 'submodules/minimap2' (https://github.com/lh3/minimap2) registered for path 'submodules/minimap2'
amazon-ebs: Submodule 'submodules/minimap2' (https://github.com/lh3/minimap2) registered for path 'submodules/minimap2'
2018/01/30 19:09:59 ui: amazon-ebs: Submodule 'submodules/racon' (https://github.com/isovic/racon) registered for path 'submodules/racon'
amazon-ebs: Submodule 'submodules/racon' (https://github.com/isovic/racon) registered for path 'submodules/racon'
2018/01/30 19:09:59 ui: amazon-ebs: Submodule 'submodules/scrappie' (https://github.com/nanoporetech/scrappie.git) registered for path 'submodules/scrappie'
amazon-ebs: Submodule 'submodules/scrappie' (https://github.com/nanoporetech/scrappie.git) registered for path 'submodules/scrappie'
2018/01/30 19:09:59 ui: amazon-ebs: Cloning into 'submodules/bwa'...
amazon-ebs: Cloning into 'submodules/bwa'...
2018/01/30 19:10:00 ui: amazon-ebs: Submodule path 'submodules/bwa': checked out '5961611c358e480110793bbf241523a3cfac049b'
amazon-ebs: Submodule path 'submodules/bwa': checked out '5961611c358e480110793bbf241523a3cfac049b'
2018/01/30 19:10:00 ui: amazon-ebs: Cloning into 'submodules/miniasm'...
amazon-ebs: Cloning into 'submodules/miniasm'...
2018/01/30 19:10:00 ui: amazon-ebs: Submodule path 'submodules/miniasm': checked out '17d5bd12290e0e8a48a5df5afaeaef4d171aa133'
amazon-ebs: Submodule path 'submodules/miniasm': checked out '17d5bd12290e0e8a48a5df5afaeaef4d171aa133'
2018/01/30 19:10:00 ui: amazon-ebs: Cloning into 'submodules/minimap2'...
amazon-ebs: Cloning into 'submodules/minimap2'...
2018/01/30 19:10:00 ui: amazon-ebs: Submodule path 'submodules/minimap2': checked out '306e4541f8a4bcc365ccb5c2817aae74b48820e5'
amazon-ebs: Submodule path 'submodules/minimap2': checked out '306e4541f8a4bcc365ccb5c2817aae74b48820e5'
2018/01/30 19:10:00 ui: amazon-ebs: Cloning into 'submodules/racon'...
amazon-ebs: Cloning into 'submodules/racon'...
2018/01/30 19:10:01 ui: amazon-ebs: Submodule path 'submodules/racon': checked out 'fdcb34ac11b9b98f5e7fb0b219c71c88793c7298'
amazon-ebs: Submodule path 'submodules/racon': checked out 'fdcb34ac11b9b98f5e7fb0b219c71c88793c7298'
2018/01/30 19:10:01 ui: amazon-ebs: Submodule 'codebase/argparser' (https://github.com/isovic/argparser.git) registered for path 'codebase/argparser'
amazon-ebs: Submodule 'codebase/argparser' (https://github.com/isovic/argparser.git) registered for path 'codebase/argparser'
2018/01/30 19:10:01 ui: amazon-ebs: Submodule 'codebase/samscripts' (https://github.com/isovic/samscripts.git) registered for path 'codebase/samscripts'
amazon-ebs: Submodule 'codebase/samscripts' (https://github.com/isovic/samscripts.git) registered for path 'codebase/samscripts'
2018/01/30 19:10:01 ui: amazon-ebs: Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib.git) registered for path 'codebase/seqlib'
amazon-ebs: Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib.git) registered for path 'codebase/seqlib'
2018/01/30 19:10:01 ui: amazon-ebs: Submodule 'codebase/spoa' (https://github.com/rvaser/spoa) registered for path 'codebase/spoa'
amazon-ebs: Submodule 'codebase/spoa' (https://github.com/rvaser/spoa) registered for path 'codebase/spoa'
2018/01/30 19:10:01 ui: amazon-ebs: Cloning into 'codebase/argparser'...
amazon-ebs: Cloning into 'codebase/argparser'...
2018/01/30 19:10:01 ui: amazon-ebs: Submodule path 'submodules/racon/codebase/argparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671'
amazon-ebs: Submodule path 'submodules/racon/codebase/argparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671'
2018/01/30 19:10:01 ui: amazon-ebs: Cloning into 'codebase/samscripts'...
amazon-ebs: Cloning into 'codebase/samscripts'...
2018/01/30 19:10:01 ui: amazon-ebs: Submodule path 'submodules/racon/codebase/samscripts': checked out 'cd7440fbbffafd76f40b15973c93acbe6111265a'
amazon-ebs: Submodule path 'submodules/racon/codebase/samscripts': checked out 'cd7440fbbffafd76f40b15973c93acbe6111265a'
2018/01/30 19:10:01 ui: amazon-ebs: Cloning into 'codebase/seqlib'...
amazon-ebs: Cloning into 'codebase/seqlib'...
2018/01/30 19:10:02 ui: amazon-ebs: Submodule path 'submodules/racon/codebase/seqlib': checked out 'b269c54358e8d54af0b0cacc88bf6ce2e6d91f3c'
amazon-ebs: Submodule path 'submodules/racon/codebase/seqlib': checked out 'b269c54358e8d54af0b0cacc88bf6ce2e6d91f3c'
2018/01/30 19:10:02 ui: amazon-ebs: Cloning into 'codebase/spoa'...
amazon-ebs: Cloning into 'codebase/spoa'...
2018/01/30 19:10:02 ui: amazon-ebs: Submodule path 'submodules/racon/codebase/spoa': checked out 'b29e10ba822c2c47dfddf3865bc6a6fea2c3d69b'
amazon-ebs: Submodule path 'submodules/racon/codebase/spoa': checked out 'b29e10ba822c2c47dfddf3865bc6a6fea2c3d69b'
2018/01/30 19:10:02 ui: amazon-ebs: Submodule 'vendor/bioparser' (https://github.com/rvaser/bioparser) registered for path 'vendor/bioparser'
amazon-ebs: Submodule 'vendor/bioparser' (https://github.com/rvaser/bioparser) registered for path 'vendor/bioparser'
2018/01/30 19:10:02 ui: amazon-ebs: Cloning into 'vendor/bioparser'...
amazon-ebs: Cloning into 'vendor/bioparser'...
2018/01/30 19:10:03 ui: amazon-ebs: Submodule path 'submodules/racon/codebase/spoa/vendor/bioparser': checked out 'bf94252ae60e7cd977279cda23cd8fedcfea86a9'
amazon-ebs: Submodule path 'submodules/racon/codebase/spoa/vendor/bioparser': checked out 'bf94252ae60e7cd977279cda23cd8fedcfea86a9'
2018/01/30 19:10:03 ui: amazon-ebs: Cloning into 'submodules/scrappie'...
amazon-ebs: Cloning into 'submodules/scrappie'...
2018/01/30 19:10:05 ui: amazon-ebs: Submodule path 'submodules/scrappie': checked out '3f5904406defbd0a15329818f675a37dcfa578c0'
amazon-ebs: Submodule path 'submodules/scrappie': checked out '3f5904406defbd0a15329818f675a37dcfa578c0'
2018/01/30 19:10:05 ui: amazon-ebs: starting make
amazon-ebs: starting make
2018/01/30 19:10:05 ui: amazon-ebs: + cd pomoxis/
amazon-ebs: + cd pomoxis/
2018/01/30 19:10:05 ui: amazon-ebs: + echo 'starting make'
amazon-ebs: + echo 'starting make'
2018/01/30 19:10:05 ui: amazon-ebs: + CFLAGS=-I/usr/include/hdf5/serial
amazon-ebs: + CFLAGS=-I/usr/include/hdf5/serial
2018/01/30 19:10:05 ui: amazon-ebs: + CPPFLAGS=-I/usr/include/hdf5/serial
amazon-ebs: + CPPFLAGS=-I/usr/include/hdf5/serial
2018/01/30 19:10:05 ui: amazon-ebs: + make V=1 install
amazon-ebs: + make V=1 install
2018/01/30 19:10:05 ui: amazon-ebs: test -d venv || virtualenv venv --python=python3
amazon-ebs: test -d venv || virtualenv venv --python=python3
2018/01/30 19:10:05 ui: amazon-ebs: Using base prefix '/home/ubuntu/anaconda'
amazon-ebs: Using base prefix '/home/ubuntu/anaconda'
2018/01/30 19:10:05 ui: amazon-ebs: New python executable in /home/ubuntu/pomoxis/venv/bin/python3
amazon-ebs: New python executable in /home/ubuntu/pomoxis/venv/bin/python3
2018/01/30 19:10:05 ui: amazon-ebs: copying /home/ubuntu/anaconda/bin/python3 => /home/ubuntu/pomoxis/venv/bin/python3
amazon-ebs: copying /home/ubuntu/anaconda/bin/python3 => /home/ubuntu/pomoxis/venv/bin/python3
2018/01/30 19:10:05 ui: amazon-ebs: Also creating executable in /home/ubuntu/pomoxis/venv/bin/python
amazon-ebs: Also creating executable in /home/ubuntu/pomoxis/venv/bin/python
2018/01/30 19:10:07 ui: amazon-ebs: Installing setuptools, pip, wheel...done.
amazon-ebs: Installing setuptools, pip, wheel...done.
2018/01/30 19:10:07 ui: amazon-ebs: Running virtualenv with interpreter /home/ubuntu/anaconda/bin/python3
amazon-ebs: Running virtualenv with interpreter /home/ubuntu/anaconda/bin/python3
2018/01/30 19:10:07 ui: amazon-ebs: . ./venv/bin/activate && pip install pip --upgrade
amazon-ebs: . ./venv/bin/activate && pip install pip --upgrade
2018/01/30 19:10:08 ui: amazon-ebs: Requirement already up-to-date: pip in ./venv/lib/python3.6/site-packages
amazon-ebs: Requirement already up-to-date: pip in ./venv/lib/python3.6/site-packages
2018/01/30 19:10:08 ui: amazon-ebs: . ./venv/bin/activate && pip install numpy # needs to get done before other things
amazon-ebs: . ./venv/bin/activate && pip install numpy # needs to get done before other things
2018/01/30 19:10:08 ui: amazon-ebs: Collecting numpy
amazon-ebs: Collecting numpy
2018/01/30 19:10:09 ui: amazon-ebs: Using cached numpy-1.14.0-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: Using cached numpy-1.14.0-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:10:09 ui: amazon-ebs: Installing collected packages: numpy
amazon-ebs: Installing collected packages: numpy
2018/01/30 19:10:10 ui: amazon-ebs: Successfully installed numpy-1.14.0
amazon-ebs: Successfully installed numpy-1.14.0
2018/01/30 19:10:10 ui: amazon-ebs: . ./venv/bin/activate && pip install -r requirements.txt
amazon-ebs: . ./venv/bin/activate && pip install -r requirements.txt
2018/01/30 19:10:11 ui: amazon-ebs: Collecting git+https://github.com/nanoporetech/nanonet@cd805595 (from -r requirements.txt (line 12))
amazon-ebs: Collecting git+https://github.com/nanoporetech/nanonet@cd805595 (from -r requirements.txt (line 12))
2018/01/30 19:10:11 ui: amazon-ebs: Cloning https://github.com/nanoporetech/nanonet (to cd805595) to /tmp/pip-z0e7eglj-build
amazon-ebs: Cloning https://github.com/nanoporetech/nanonet (to cd805595) to /tmp/pip-z0e7eglj-build
2018/01/30 19:10:11 ui: amazon-ebs: Could not find a tag or branch 'cd805595', assuming commit.
amazon-ebs: Could not find a tag or branch 'cd805595', assuming commit.
2018/01/30 19:10:12 ui: amazon-ebs: Collecting git+https://github.com/rrwick/Porechop (from -r requirements.txt (line 13))
amazon-ebs: Collecting git+https://github.com/rrwick/Porechop (from -r requirements.txt (line 13))
2018/01/30 19:10:12 ui: amazon-ebs: Cloning https://github.com/rrwick/Porechop to /tmp/pip-vz1extmr-build
amazon-ebs: Cloning https://github.com/rrwick/Porechop to /tmp/pip-vz1extmr-build
2018/01/30 19:10:13 ui: amazon-ebs: Collecting aiozmq (from -r requirements.txt (line 3))
amazon-ebs: Collecting aiozmq (from -r requirements.txt (line 3))
2018/01/30 19:10:13 ui: amazon-ebs: Downloading aiozmq-0.7.1-py3-none-any.whl
amazon-ebs: Downloading aiozmq-0.7.1-py3-none-any.whl
2018/01/30 19:10:13 ui: amazon-ebs: Collecting biopython>=1.63 (from -r requirements.txt (line 4))
amazon-ebs: Collecting biopython>=1.63 (from -r requirements.txt (line 4))
2018/01/30 19:10:13 ui: amazon-ebs: Downloading biopython-1.70-cp36-cp36m-manylinux1_x86_64.whl (2.2MB)
amazon-ebs: Downloading biopython-1.70-cp36-cp36m-manylinux1_x86_64.whl (2.2MB)
2018/01/30 19:10:14 ui: amazon-ebs: Collecting cffi (from -r requirements.txt (line 5))
amazon-ebs: Collecting cffi (from -r requirements.txt (line 5))
2018/01/30 19:10:14 ui: amazon-ebs: Downloading cffi-1.11.4-cp36-cp36m-manylinux1_x86_64.whl (420kB)
amazon-ebs: Downloading cffi-1.11.4-cp36-cp36m-manylinux1_x86_64.whl (420kB)
2018/01/30 19:10:14 ui: amazon-ebs: Collecting fast5_research (from -r requirements.txt (line 6))
amazon-ebs: Collecting fast5_research (from -r requirements.txt (line 6))
2018/01/30 19:10:14 ui: amazon-ebs: Downloading fast5_research-1.0.7.tar.gz
amazon-ebs: Downloading fast5_research-1.0.7.tar.gz
2018/01/30 19:10:14 ui: amazon-ebs: Collecting msgpack-python (from -r requirements.txt (line 7))
amazon-ebs: Collecting msgpack-python (from -r requirements.txt (line 7))
2018/01/30 19:10:14 ui: amazon-ebs: Downloading msgpack-python-0.5.1.tar.gz (138kB)
amazon-ebs: Downloading msgpack-python-0.5.1.tar.gz (138kB)
2018/01/30 19:10:14 ui: amazon-ebs: Requirement already satisfied: numpy in ./venv/lib/python3.6/site-packages (from -r requirements.txt (line 8))
amazon-ebs: Requirement already satisfied: numpy in ./venv/lib/python3.6/site-packages (from -r requirements.txt (line 8))
2018/01/30 19:10:14 ui: amazon-ebs: Collecting pysam (from -r requirements.txt (line 9))
amazon-ebs: Collecting pysam (from -r requirements.txt (line 9))
2018/01/30 19:10:14 ui: amazon-ebs: Downloading pysam-0.13-cp36-cp36m-manylinux1_x86_64.whl (9.3MB)
amazon-ebs: Downloading pysam-0.13-cp36-cp36m-manylinux1_x86_64.whl (9.3MB)
2018/01/30 19:10:15 ui: amazon-ebs: Collecting sphinx-argparse (from -r requirements.txt (line 10))
amazon-ebs: Collecting sphinx-argparse (from -r requirements.txt (line 10))
2018/01/30 19:10:15 ui: amazon-ebs: Downloading sphinx-argparse-0.2.1.tar.gz
amazon-ebs: Downloading sphinx-argparse-0.2.1.tar.gz
2018/01/30 19:10:16 ui: amazon-ebs: Collecting watchdog (from -r requirements.txt (line 11))
amazon-ebs: Collecting watchdog (from -r requirements.txt (line 11))
2018/01/30 19:10:16 ui: amazon-ebs: Downloading watchdog-0.8.3.tar.gz (83kB)
amazon-ebs: Downloading watchdog-0.8.3.tar.gz (83kB)
2018/01/30 19:10:16 ui: amazon-ebs: Collecting future (from nanonet==2.0.0->-r requirements.txt (line 12))
amazon-ebs: Collecting future (from nanonet==2.0.0->-r requirements.txt (line 12))
2018/01/30 19:10:16 ui: amazon-ebs: Downloading future-0.16.0.tar.gz (824kB)
amazon-ebs: Downloading future-0.16.0.tar.gz (824kB)
2018/01/30 19:10:16 ui: amazon-ebs: Collecting h5py (from nanonet==2.0.0->-r requirements.txt (line 12))
amazon-ebs: Collecting h5py (from nanonet==2.0.0->-r requirements.txt (line 12))
2018/01/30 19:10:17 ui: amazon-ebs: Using cached h5py-2.7.1-cp36-cp36m-manylinux1_x86_64.whl
amazon-ebs: Using cached h5py-2.7.1-cp36-cp36m-manylinux1_x86_64.whl
2018/01/30 19:10:17 ui: amazon-ebs: Collecting myriad>=0.1.2 (from nanonet==2.0.0->-r requirements.txt (line 12))
amazon-ebs: Collecting myriad>=0.1.2 (from nanonet==2.0.0->-r requirements.txt (line 12))
2018/01/30 19:10:17 ui: amazon-ebs: Downloading myriad-0.1.4.zip
amazon-ebs: Downloading myriad-0.1.4.zip
2018/01/30 19:10:17 ui: amazon-ebs: Collecting pyzmq>=13.1 (from aiozmq->-r requirements.txt (line 3))
amazon-ebs: Collecting pyzmq>=13.1 (from aiozmq->-r requirements.txt (line 3))
2018/01/30 19:10:17 ui: amazon-ebs: Downloading pyzmq-16.0.4-cp36-cp36m-manylinux1_x86_64.whl (3.1MB)
amazon-ebs: Downloading pyzmq-16.0.4-cp36-cp36m-manylinux1_x86_64.whl (3.1MB)
2018/01/30 19:10:18 ui: amazon-ebs: Collecting pycparser (from cffi->-r requirements.txt (line 5))
amazon-ebs: Collecting pycparser (from cffi->-r requirements.txt (line 5))
2018/01/30 19:10:18 ui: amazon-ebs: Downloading pycparser-2.18.tar.gz (245kB)
amazon-ebs: Downloading pycparser-2.18.tar.gz (245kB)
2018/01/30 19:10:18 ui: amazon-ebs: Collecting progressbar2 (from fast5_research->-r requirements.txt (line 6))
amazon-ebs: Collecting progressbar2 (from fast5_research->-r requirements.txt (line 6))
2018/01/30 19:10:18 ui: amazon-ebs: Downloading progressbar2-3.34.3-py2.py3-none-any.whl
amazon-ebs: Downloading progressbar2-3.34.3-py2.py3-none-any.whl
2018/01/30 19:10:18 ui: amazon-ebs: Collecting sphinx (from sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting sphinx (from sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:18 ui: amazon-ebs: Downloading Sphinx-1.6.6-py2.py3-none-any.whl (1.9MB)
amazon-ebs: Downloading Sphinx-1.6.6-py2.py3-none-any.whl (1.9MB)
2018/01/30 19:10:18 ui: amazon-ebs: Collecting CommonMark>=0.5.6 (from sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting CommonMark>=0.5.6 (from sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:18 ui: amazon-ebs: Downloading CommonMark-0.7.4-py2.py3-none-any.whl (46kB)
amazon-ebs: Downloading CommonMark-0.7.4-py2.py3-none-any.whl (46kB)
2018/01/30 19:10:18 ui: amazon-ebs: Collecting PyYAML>=3.10 (from watchdog->-r requirements.txt (line 11))
amazon-ebs: Collecting PyYAML>=3.10 (from watchdog->-r requirements.txt (line 11))
2018/01/30 19:10:18 ui: amazon-ebs: Downloading PyYAML-3.12.tar.gz (253kB)
amazon-ebs: Downloading PyYAML-3.12.tar.gz (253kB)
2018/01/30 19:10:19 ui: amazon-ebs: Collecting argh>=0.24.1 (from watchdog->-r requirements.txt (line 11))
amazon-ebs: Collecting argh>=0.24.1 (from watchdog->-r requirements.txt (line 11))
2018/01/30 19:10:19 ui: amazon-ebs: Downloading argh-0.26.2-py2.py3-none-any.whl
amazon-ebs: Downloading argh-0.26.2-py2.py3-none-any.whl
2018/01/30 19:10:19 ui: amazon-ebs: Collecting pathtools>=0.1.1 (from watchdog->-r requirements.txt (line 11))
amazon-ebs: Collecting pathtools>=0.1.1 (from watchdog->-r requirements.txt (line 11))
2018/01/30 19:10:19 ui: amazon-ebs: Downloading pathtools-0.1.2.tar.gz
amazon-ebs: Downloading pathtools-0.1.2.tar.gz
2018/01/30 19:10:19 ui: amazon-ebs: Collecting six (from h5py->nanonet==2.0.0->-r requirements.txt (line 12))
amazon-ebs: Collecting six (from h5py->nanonet==2.0.0->-r requirements.txt (line 12))
2018/01/30 19:10:19 ui: amazon-ebs: Using cached six-1.11.0-py2.py3-none-any.whl
amazon-ebs: Using cached six-1.11.0-py2.py3-none-any.whl
2018/01/30 19:10:19 ui: amazon-ebs: Collecting python-utils>=2.1.0 (from progressbar2->fast5_research->-r requirements.txt (line 6))
amazon-ebs: Collecting python-utils>=2.1.0 (from progressbar2->fast5_research->-r requirements.txt (line 6))
2018/01/30 19:10:20 ui: amazon-ebs: Downloading python_utils-2.2.0-py2.py3-none-any.whl
amazon-ebs: Downloading python_utils-2.2.0-py2.py3-none-any.whl
2018/01/30 19:10:20 ui: amazon-ebs: Collecting snowballstemmer>=1.1 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting snowballstemmer>=1.1 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:20 ui: amazon-ebs: Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
amazon-ebs: Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
2018/01/30 19:10:20 ui: amazon-ebs: Collecting alabaster<0.8,>=0.7 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting alabaster<0.8,>=0.7 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:20 ui: amazon-ebs: Downloading alabaster-0.7.10-py2.py3-none-any.whl
amazon-ebs: Downloading alabaster-0.7.10-py2.py3-none-any.whl
2018/01/30 19:10:20 ui: amazon-ebs: Collecting docutils>=0.11 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting docutils>=0.11 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:20 ui: amazon-ebs: Downloading docutils-0.14-py3-none-any.whl (543kB)
amazon-ebs: Downloading docutils-0.14-py3-none-any.whl (543kB)
2018/01/30 19:10:20 ui: amazon-ebs: Collecting babel!=2.0,>=1.3 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting babel!=2.0,>=1.3 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:20 ui: amazon-ebs: Downloading Babel-2.5.3-py2.py3-none-any.whl (6.8MB)
amazon-ebs: Downloading Babel-2.5.3-py2.py3-none-any.whl (6.8MB)
2018/01/30 19:10:21 ui: amazon-ebs: Collecting Jinja2>=2.3 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting Jinja2>=2.3 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading Jinja2-2.10-py2.py3-none-any.whl (126kB)
amazon-ebs: Downloading Jinja2-2.10-py2.py3-none-any.whl (126kB)
2018/01/30 19:10:21 ui: amazon-ebs: Collecting Pygments>=2.0 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting Pygments>=2.0 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB)
amazon-ebs: Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB)
2018/01/30 19:10:21 ui: amazon-ebs: Requirement already satisfied: setuptools in ./venv/lib/python3.6/site-packages (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Requirement already satisfied: setuptools in ./venv/lib/python3.6/site-packages (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Collecting sphinxcontrib-websupport (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting sphinxcontrib-websupport (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading sphinxcontrib_websupport-1.0.1-py2.py3-none-any.whl
amazon-ebs: Downloading sphinxcontrib_websupport-1.0.1-py2.py3-none-any.whl
2018/01/30 19:10:21 ui: amazon-ebs: Collecting requests>=2.0.0 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting requests>=2.0.0 (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading requests-2.18.4-py2.py3-none-any.whl (88kB)
amazon-ebs: Downloading requests-2.18.4-py2.py3-none-any.whl (88kB)
2018/01/30 19:10:21 ui: amazon-ebs: Collecting imagesize (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting imagesize (from sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading imagesize-0.7.1-py2.py3-none-any.whl
amazon-ebs: Downloading imagesize-0.7.1-py2.py3-none-any.whl
2018/01/30 19:10:21 ui: amazon-ebs: Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading pytz-2017.3-py2.py3-none-any.whl (511kB)
amazon-ebs: Downloading pytz-2017.3-py2.py3-none-any.whl (511kB)
2018/01/30 19:10:21 ui: amazon-ebs: Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:21 ui: amazon-ebs: Downloading MarkupSafe-1.0.tar.gz
amazon-ebs: Downloading MarkupSafe-1.0.tar.gz
2018/01/30 19:10:22 ui: amazon-ebs: Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:22 ui: amazon-ebs: Downloading idna-2.6-py2.py3-none-any.whl (56kB)
amazon-ebs: Downloading idna-2.6-py2.py3-none-any.whl (56kB)
2018/01/30 19:10:22 ui: amazon-ebs: Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:22 ui: amazon-ebs: Downloading certifi-2018.1.18-py2.py3-none-any.whl (151kB)
amazon-ebs: Downloading certifi-2018.1.18-py2.py3-none-any.whl (151kB)
2018/01/30 19:10:22 ui: amazon-ebs: Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:22 ui: amazon-ebs: Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB)
amazon-ebs: Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB)
2018/01/30 19:10:22 ui: amazon-ebs: Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
amazon-ebs: Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx->sphinx-argparse->-r requirements.txt (line 10))
2018/01/30 19:10:22 ui: amazon-ebs: Downloading urllib3-1.22-py2.py3-none-any.whl (132kB)
amazon-ebs: Downloading urllib3-1.22-py2.py3-none-any.whl (132kB)
2018/01/30 19:10:22 ui: amazon-ebs: Building wheels for collected packages: fast5-research, msgpack-python, sphinx-argparse, watchdog, future, myriad, pycparser, PyYAML, pathtools, MarkupSafe
amazon-ebs: Building wheels for collected packages: fast5-research, msgpack-python, sphinx-argparse, watchdog, future, myriad, pycparser, PyYAML, pathtools, MarkupSafe
2018/01/30 19:10:22 ui: amazon-ebs: Running setup.py bdist_wheel for fast5-research: started
amazon-ebs: Running setup.py bdist_wheel for fast5-research: started
2018/01/30 19:10:22 ui: amazon-ebs: Running setup.py bdist_wheel for fast5-research: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for fast5-research: finished with status 'done'
2018/01/30 19:10:22 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/f2/2a/2a/f8051acf2855c381e3f1ad49be5e6245c29469005bbc4e12c2
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/f2/2a/2a/f8051acf2855c381e3f1ad49be5e6245c29469005bbc4e12c2
2018/01/30 19:10:22 ui: amazon-ebs: Running setup.py bdist_wheel for msgpack-python: started
amazon-ebs: Running setup.py bdist_wheel for msgpack-python: started
amazon-ebs: Running setup.py bdist_wheel for msgpack-python: finished with status 'done'
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/14/68/75/0b7d95841ed4f67f48b112af77154c727c1957ca673d5d1695
2018/01/30 19:10:27 ui: amazon-ebs: Running setup.py bdist_wheel for msgpack-python: finished with status 'done'
2018/01/30 19:10:27 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/14/68/75/0b7d95841ed4f67f48b112af77154c727c1957ca673d5d1695
2018/01/30 19:10:27 ui: amazon-ebs: Running setup.py bdist_wheel for sphinx-argparse: started
amazon-ebs: Running setup.py bdist_wheel for sphinx-argparse: started
2018/01/30 19:10:27 ui: amazon-ebs: Running setup.py bdist_wheel for sphinx-argparse: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for sphinx-argparse: finished with status 'done'
2018/01/30 19:10:27 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/fa/7b/34/8ce404e35a487b6e5178ac4637c480ab98768e0f8efab8f9ed
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/fa/7b/34/8ce404e35a487b6e5178ac4637c480ab98768e0f8efab8f9ed
2018/01/30 19:10:27 ui: amazon-ebs: Running setup.py bdist_wheel for watchdog: started
amazon-ebs: Running setup.py bdist_wheel for watchdog: started
2018/01/30 19:10:27 ui: amazon-ebs: Running setup.py bdist_wheel for watchdog: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for watchdog: finished with status 'done'
2018/01/30 19:10:27 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/3c/9c/be/e82ae5a37c19baf8abe88623d1f47d2d502bed7b54d4f34740
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/3c/9c/be/e82ae5a37c19baf8abe88623d1f47d2d502bed7b54d4f34740
2018/01/30 19:10:27 ui: amazon-ebs: Running setup.py bdist_wheel for future: started
amazon-ebs: Running setup.py bdist_wheel for future: started
2018/01/30 19:10:28 ui: amazon-ebs: Running setup.py bdist_wheel for future: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for future: finished with status 'done'
2018/01/30 19:10:28 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/c2/50/7c/0d83b4baac4f63ff7a765bd16390d2ab43c93587fac9d6017a
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/c2/50/7c/0d83b4baac4f63ff7a765bd16390d2ab43c93587fac9d6017a
2018/01/30 19:10:28 ui: amazon-ebs: Running setup.py bdist_wheel for myriad: started
amazon-ebs: Running setup.py bdist_wheel for myriad: started
2018/01/30 19:10:28 ui: amazon-ebs: Running setup.py bdist_wheel for myriad: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for myriad: finished with status 'done'
2018/01/30 19:10:28 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/f1/30/7a/545d430d32d725ad85df95f4c6971dcee513be919b23478760
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/f1/30/7a/545d430d32d725ad85df95f4c6971dcee513be919b23478760
2018/01/30 19:10:28 ui: amazon-ebs: Running setup.py bdist_wheel for pycparser: started
amazon-ebs: Running setup.py bdist_wheel for pycparser: started
2018/01/30 19:10:28 ui: amazon-ebs: Running setup.py bdist_wheel for pycparser: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for pycparser: finished with status 'done'
2018/01/30 19:10:28 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/95/14/9a/5e7b9024459d2a6600aaa64e0ba485325aff7a9ac7489db1b6
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/95/14/9a/5e7b9024459d2a6600aaa64e0ba485325aff7a9ac7489db1b6
2018/01/30 19:10:28 ui: amazon-ebs: Running setup.py bdist_wheel for PyYAML: started
amazon-ebs: Running setup.py bdist_wheel for PyYAML: started
2018/01/30 19:10:29 ui: amazon-ebs: Running setup.py bdist_wheel for PyYAML: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for PyYAML: finished with status 'done'
2018/01/30 19:10:29 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/2c/f7/79/13f3a12cd723892437c0cfbde1230ab4d82947ff7b3839a4fc
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/2c/f7/79/13f3a12cd723892437c0cfbde1230ab4d82947ff7b3839a4fc
2018/01/30 19:10:29 ui: amazon-ebs: Running setup.py bdist_wheel for pathtools: started
amazon-ebs: Running setup.py bdist_wheel for pathtools: started
2018/01/30 19:10:29 ui: amazon-ebs: Running setup.py bdist_wheel for pathtools: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for pathtools: finished with status 'done'
2018/01/30 19:10:29 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/60/0d/2a/ffe065d190b580be6af9a862c68ed6a8a89c1778bd5c7ba7b8
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/60/0d/2a/ffe065d190b580be6af9a862c68ed6a8a89c1778bd5c7ba7b8
2018/01/30 19:10:29 ui: amazon-ebs: Running setup.py bdist_wheel for MarkupSafe: started
amazon-ebs: Running setup.py bdist_wheel for MarkupSafe: started
2018/01/30 19:10:30 ui: amazon-ebs: Running setup.py bdist_wheel for MarkupSafe: finished with status 'done'
amazon-ebs: Running setup.py bdist_wheel for MarkupSafe: finished with status 'done'
2018/01/30 19:10:30 ui: amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57
amazon-ebs: Stored in directory: /home/ubuntu/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57
2018/01/30 19:10:30 ui: amazon-ebs: Successfully built fast5-research msgpack-python sphinx-argparse watchdog future myriad pycparser PyYAML pathtools MarkupSafe
amazon-ebs: Successfully built fast5-research msgpack-python sphinx-argparse watchdog future myriad pycparser PyYAML pathtools MarkupSafe
2018/01/30 19:10:30 ui: amazon-ebs: Installing collected packages: pyzmq, aiozmq, biopython, pycparser, cffi, six, h5py, python-utils, progressbar2, fast5-research, msgpack-python, pysam, snowballstemmer, alabaster, docutils, pytz, babel, MarkupSafe, Jinja2, Pygments, sphinxcontrib-websupport, idna, certifi, chardet, urllib3, requests, imagesize, sphinx, future, CommonMark, sphinx-argparse, PyYAML, argh, pathtools, watchdog, myriad, nanonet, porechop
amazon-ebs: Installing collected packages: pyzmq, aiozmq, biopython, pycparser, cffi, six, h5py, python-utils, progressbar2, fast5-research, msgpack-python, pysam, snowballstemmer, alabaster, docutils, pytz, babel, MarkupSafe, Jinja2, Pygments, sphinxcontrib-websupport, idna, certifi, chardet, urllib3, requests, imagesize, sphinx, future, CommonMark, sphinx-argparse, PyYAML, argh, pathtools, watchdog, myriad, nanonet, porechop
2018/01/30 19:10:33 ui: amazon-ebs: Running setup.py install for nanonet: started
amazon-ebs: Running setup.py install for nanonet: started
2018/01/30 19:10:34 ui: amazon-ebs: Running setup.py install for nanonet: finished with status 'done'
amazon-ebs: Running setup.py install for nanonet: finished with status 'done'
2018/01/30 19:10:34 ui: amazon-ebs: Running setup.py install for porechop: started
amazon-ebs: Running setup.py install for porechop: started
2018/01/30 19:10:39 ui: amazon-ebs: Running setup.py install for porechop: finished with status 'done'
amazon-ebs: Running setup.py install for porechop: finished with status 'done'
2018/01/30 19:10:40 ui: amazon-ebs: Successfully installed CommonMark-0.7.4 Jinja2-2.10 MarkupSafe-1.0 PyYAML-3.12 Pygments-2.2.0 aiozmq-0.7.1 alabaster-0.7.10 argh-0.26.2 babel-2.5.3 biopython-1.70 certifi-2018.1.18 cffi-1.11.4 chardet-3.0.4 docutils-0.14 fast5-research-1.0.7 future-0.16.0 h5py-2.7.1 idna-2.6 imagesize-0.7.1 msgpack-python-0.5.1 myriad-0.1.4 nanonet-2.0.0 pathtools-0.1.2 porechop-0.2.3 progressbar2-3.34.3 pycparser-2.18 pysam-0.13 python-utils-2.2.0 pytz-2017.3 pyzmq-16.0.4 requests-2.18.4 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.6.6 sphinx-argparse-0.2.1 sphinxcontrib-websupport-1.0.1 urllib3-1.22 watchdog-0.8.3
amazon-ebs: Successfully installed CommonMark-0.7.4 Jinja2-2.10 MarkupSafe-1.0 PyYAML-3.12 Pygments-2.2.0 aiozmq-0.7.1 alabaster-0.7.10 argh-0.26.2 babel-2.5.3 biopython-1.70 certifi-2018.1.18 cffi-1.11.4 chardet-3.0.4 docutils-0.14 fast5-research-1.0.7 future-0.16.0 h5py-2.7.1 idna-2.6 imagesize-0.7.1 msgpack-python-0.5.1 myriad-0.1.4 nanonet-2.0.0 pathtools-0.1.2 porechop-0.2.3 progressbar2-3.34.3 pycparser-2.18 pysam-0.13 python-utils-2.2.0 pytz-2017.3 pyzmq-16.0.4 requests-2.18.4 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.6.6 sphinx-argparse-0.2.1 sphinxcontrib-websupport-1.0.1 urllib3-1.22 watchdog-0.8.3
2018/01/30 19:10:40 ui: amazon-ebs: mkdir -p bincache
amazon-ebs: mkdir -p bincache
2018/01/30 19:10:40 ui: amazon-ebs: Making minimap2
amazon-ebs: Making minimap2
2018/01/30 19:10:40 ui: amazon-ebs: cd submodules/minimap2 && make
amazon-ebs: cd submodules/minimap2 && make
2018/01/30 19:10:40 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/minimap2'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/minimap2'
2018/01/30 19:10:40 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC main.c -o main.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC main.c -o main.o
2018/01/30 19:10:40 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC getopt.c -o getopt.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC getopt.c -o getopt.o
2018/01/30 19:10:40 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o
2018/01/30 19:10:40 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o
2018/01/30 19:10:40 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o
2018/01/30 19:10:40 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o
2018/01/30 19:10:41 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sketch.c -o sketch.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sketch.c -o sketch.o
2018/01/30 19:10:41 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sdust.c -o sdust.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sdust.c -o sdust.o
2018/01/30 19:10:41 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC index.c -o index.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC index.c -o index.o
2018/01/30 19:10:41 ui: amazon-ebs: index.c: In function ‘mm_idx_load’:
amazon-ebs: index.c: In function ‘mm_idx_load’:
2018/01/30 19:10:41 ui: amazon-ebs: index.c:396:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:396:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(&l, 1, 1, fp);
amazon-ebs: fread(&l, 1, 1, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:398:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:398:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(s->name, 1, l, fp);
amazon-ebs: fread(s->name, 1, l, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:400:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:400:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(&s->len, 4, 1, fp);
amazon-ebs: fread(&s->len, 4, 1, fp);
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:409:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:409:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(&b->n, 4, 1, fp);
amazon-ebs: fread(&b->n, 4, 1, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:411:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:411:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(b->p, 8, b->n, fp);
amazon-ebs: fread(b->p, 8, b->n, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:412:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:412:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(&size, 4, 1, fp);
amazon-ebs: fread(&size, 4, 1, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:419:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:419:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(x, 8, 2, fp);
amazon-ebs: fread(x, 8, 2, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: index.c:426:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:426:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:41 ui: amazon-ebs: fread(mi->S, 4, (sum_len + 7) / 8, fp);
amazon-ebs: fread(mi->S, 4, (sum_len + 7) / 8, fp);
2018/01/30 19:10:41 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:41 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC chain.c -o chain.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC chain.c -o chain.o
2018/01/30 19:10:41 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC align.c -o align.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC align.c -o align.o
2018/01/30 19:10:42 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC hit.c -o hit.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC hit.c -o hit.o
2018/01/30 19:10:42 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC map.c -o map.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC map.c -o map.o
2018/01/30 19:10:43 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC format.c -o format.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC format.c -o format.o
2018/01/30 19:10:43 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC pe.c -o pe.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC pe.c -o pe.o
2018/01/30 19:10:43 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o
2018/01/30 19:10:43 ui: amazon-ebs: cc -c -msse4 -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
amazon-ebs: cc -c -msse4 -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
2018/01/30 19:10:44 ui: amazon-ebs: cc -c -msse4 -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
amazon-ebs: cc -c -msse4 -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
2018/01/30 19:10:44 ui: amazon-ebs: cc -c -msse4 -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
amazon-ebs: cc -c -msse4 -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
2018/01/30 19:10:44 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
2018/01/30 19:10:45 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
2018/01/30 19:10:45 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
2018/01/30 19:10:46 ui: amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o
amazon-ebs: cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o
2018/01/30 19:10:46 ui: amazon-ebs: ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o pe.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
amazon-ebs: ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o pe.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
2018/01/30 19:10:46 ui: amazon-ebs: ar: `u' modifier ignored since `D' is the default (see `U')
amazon-ebs: ar: `u' modifier ignored since `D' is the default (see `U')
2018/01/30 19:10:46 ui: amazon-ebs: cc -g -Wall -O2 -Wc++-compat main.o getopt.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
amazon-ebs: cc -g -Wall -O2 -Wc++-compat main.o getopt.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
2018/01/30 19:10:46 ui: amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/minimap2'
amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/minimap2'
2018/01/30 19:10:46 ui: amazon-ebs: cp submodules/minimap2/minimap2 bincache/minimap2
amazon-ebs: cp submodules/minimap2/minimap2 bincache/minimap2
amazon-ebs: Making miniasm
2018/01/30 19:10:46 ui: amazon-ebs: Making miniasm
2018/01/30 19:10:46 ui: amazon-ebs: cd submodules/miniasm && make
amazon-ebs: cd submodules/miniasm && make
2018/01/30 19:10:46 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/miniasm'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/miniasm'
2018/01/30 19:10:46 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sys.c -o sys.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sys.c -o sys.o
2018/01/30 19:10:46 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sdict.c -o sdict.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sdict.c -o sdict.o
2018/01/30 19:10:46 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. paf.c -o paf.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. paf.c -o paf.o
2018/01/30 19:10:46 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asg.c -o asg.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asg.c -o asg.o
2018/01/30 19:10:46 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. common.c -o common.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. common.c -o common.o
2018/01/30 19:10:47 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. hit.c -o hit.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. hit.c -o hit.o
2018/01/30 19:10:47 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asm.c -o asm.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asm.c -o asm.o
2018/01/30 19:10:47 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. main.c -o main.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. main.c -o main.o
2018/01/30 19:10:47 ui: amazon-ebs: gcc -g -Wall -O2 -Wc++-compat sys.o sdict.o paf.o asg.o common.o hit.o asm.o main.o -o miniasm -lm -lz -lpthread
amazon-ebs: gcc -g -Wall -O2 -Wc++-compat sys.o sdict.o paf.o asg.o common.o hit.o asm.o main.o -o miniasm -lm -lz -lpthread
2018/01/30 19:10:47 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. dotter.c -o dotter.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. dotter.c -o dotter.o
2018/01/30 19:10:48 ui: amazon-ebs: gcc -g -Wall -O2 -Wc++-compat paf.o sdict.o dotter.o -o minidot -lm -lz -lpthread
amazon-ebs: gcc -g -Wall -O2 -Wc++-compat paf.o sdict.o dotter.o -o minidot -lm -lz -lpthread
2018/01/30 19:10:48 ui: amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/miniasm'
amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/miniasm'
2018/01/30 19:10:48 ui: amazon-ebs: cp submodules/miniasm/miniasm bincache/miniasm
amazon-ebs: cp submodules/miniasm/miniasm bincache/miniasm
2018/01/30 19:10:48 ui: amazon-ebs: Making bwa
amazon-ebs: Making bwa
2018/01/30 19:10:48 ui: amazon-ebs: cd submodules/bwa && make
amazon-ebs: cd submodules/bwa && make
2018/01/30 19:10:48 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/bwa'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/bwa'
2018/01/30 19:10:48 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
2018/01/30 19:10:48 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
2018/01/30 19:10:48 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
2018/01/30 19:10:48 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
2018/01/30 19:10:49 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
2018/01/30 19:10:49 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
2018/01/30 19:10:49 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
2018/01/30 19:10:50 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
2018/01/30 19:10:52 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
2018/01/30 19:10:52 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
2018/01/30 19:10:52 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
2018/01/30 19:10:52 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
2018/01/30 19:10:53 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
2018/01/30 19:10:53 ui: amazon-ebs: bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
amazon-ebs: bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
2018/01/30 19:10:53 ui: amazon-ebs: bwt_gen.c:878:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
amazon-ebs: bwt_gen.c:878:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
2018/01/30 19:10:53 ui: amazon-ebs: bgint_t oldInverseSa0RelativeRank = 0;
amazon-ebs: bgint_t oldInverseSa0RelativeRank = 0;
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: bwt_gen.c: In function ‘BWTIncMergeBwt’:
amazon-ebs: bwt_gen.c: In function ‘BWTIncMergeBwt’:
2018/01/30 19:10:53 ui: amazon-ebs: bwt_gen.c:952:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
amazon-ebs: bwt_gen.c:952:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
2018/01/30 19:10:53 ui: amazon-ebs: unsigned int bitsInWordMinusBitPerChar;
amazon-ebs: unsigned int bitsInWordMinusBitPerChar;
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o
2018/01/30 19:10:53 ui: amazon-ebs: rope.c: In function ‘rope_restore_node’:
amazon-ebs: rope.c: In function ‘rope_restore_node’:
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(&is_bottom, 1, 1, fp);
amazon-ebs: fread(&is_bottom, 1, 1, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(&n, 2, 1, fp);
amazon-ebs: fread(&n, 2, 1, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(p[i].c, 8, 6, fp);
amazon-ebs: fread(p[i].c, 8, 6, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(q, 2, 1, fp);
amazon-ebs: fread(q, 2, 1, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:293:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:293:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(q + 1, 1, *q, fp);
amazon-ebs: fread(q + 1, 1, *q, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: rope.c: In function ‘rope_restore’:
amazon-ebs: rope.c: In function ‘rope_restore’:
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(&r->max_nodes, 4, 1, fp);
amazon-ebs: fread(&r->max_nodes, 4, 1, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: rope.c:313:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: rope.c:313:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:53 ui: amazon-ebs: fread(&r->block_len, 4, 1, fp);
amazon-ebs: fread(&r->block_len, 4, 1, fp);
2018/01/30 19:10:53 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:53 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o
2018/01/30 19:10:53 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
2018/01/30 19:10:54 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
2018/01/30 19:10:54 ui: amazon-ebs: ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
amazon-ebs: ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
2018/01/30 19:10:54 ui: amazon-ebs: ar: `u' modifier ignored since `D' is the default (see `U')
amazon-ebs: ar: `u' modifier ignored since `D' is the default (see `U')
2018/01/30 19:10:54 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o
2018/01/30 19:10:54 ui: amazon-ebs: bwashm.c: In function ‘bwa_shm_stage’:
amazon-ebs: bwashm.c: In function ‘bwa_shm_stage’:
2018/01/30 19:10:54 ui: amazon-ebs: bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:54 ui: amazon-ebs: ftruncate(shmid, BWA_CTL_SIZE);
amazon-ebs: ftruncate(shmid, BWA_CTL_SIZE);
2018/01/30 19:10:54 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:10:54 ui: amazon-ebs: bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:10:54 ui: amazon-ebs: ftruncate(shmid, idx->l_mem);
amazon-ebs: ftruncate(shmid, idx->l_mem);
amazon-ebs: ^
2018/01/30 19:10:54 ui: amazon-ebs: ^
2018/01/30 19:10:54 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
2018/01/30 19:10:54 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
2018/01/30 19:10:54 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
2018/01/30 19:10:55 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
2018/01/30 19:10:55 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
2018/01/30 19:10:55 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
2018/01/30 19:10:55 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
2018/01/30 19:10:55 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
2018/01/30 19:10:56 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o
2018/01/30 19:10:56 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
2018/01/30 19:10:57 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
2018/01/30 19:10:57 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
2018/01/30 19:10:57 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
2018/01/30 19:10:57 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
2018/01/30 19:10:57 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
2018/01/30 19:10:58 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
2018/01/30 19:10:58 ui: amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o
amazon-ebs: gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o
2018/01/30 19:10:58 ui: amazon-ebs: gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
amazon-ebs: gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
2018/01/30 19:10:58 ui: amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/bwa'
amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/bwa'
2018/01/30 19:10:58 ui: amazon-ebs: cp submodules/bwa/bwa bincache/bwa
amazon-ebs: cp submodules/bwa/bwa bincache/bwa
2018/01/30 19:10:58 ui: amazon-ebs: Making racon
amazon-ebs: Making racon
2018/01/30 19:10:58 ui: amazon-ebs: cd submodules/racon && make modules && make tools && make -j
amazon-ebs: cd submodules/racon && make modules && make tools && make -j
2018/01/30 19:10:58 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/racon'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/racon'
2018/01/30 19:10:58 ui: amazon-ebs: git submodule update --init --recursive
amazon-ebs: git submodule update --init --recursive
2018/01/30 19:10:58 ui: amazon-ebs: cd codebase/spoa && git checkout overlap
amazon-ebs: cd codebase/spoa && git checkout overlap
2018/01/30 19:10:58 ui: amazon-ebs: Previous HEAD position was b29e10b... Submodule update
amazon-ebs: Previous HEAD position was b29e10b... Submodule update
2018/01/30 19:10:58 ui: amazon-ebs: Branch overlap set up to track remote branch overlap from origin.
amazon-ebs: Branch overlap set up to track remote branch overlap from origin.
2018/01/30 19:10:58 ui: amazon-ebs: Switched to a new branch 'overlap'
amazon-ebs: Switched to a new branch 'overlap'
2018/01/30 19:10:58 ui: amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon'
amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon'
2018/01/30 19:10:58 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/racon'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/racon'
2018/01/30 19:10:58 ui: amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/isovic/graphmap.git; cd graphmap && make modules && make -j
amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/isovic/graphmap.git; cd graphmap && make modules && make -j
2018/01/30 19:10:58 ui: amazon-ebs: Cloning into 'graphmap'...
amazon-ebs: Cloning into 'graphmap'...
2018/01/30 19:10:59 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:10:59 ui: amazon-ebs: git submodule update --init --recursive
amazon-ebs: git submodule update --init --recursive
2018/01/30 19:10:59 ui: amazon-ebs: Submodule 'codebase/argumentparser' (https://github.com/isovic/argumentparser.git) registered for path 'codebase/argumentparser'
amazon-ebs: Submodule 'codebase/argumentparser' (https://github.com/isovic/argumentparser.git) registered for path 'codebase/argumentparser'
2018/01/30 19:10:59 ui: amazon-ebs: Submodule 'codebase/gindex' (https://github.com/isovic/gindex) registered for path 'codebase/gindex'
amazon-ebs: Submodule 'codebase/gindex' (https://github.com/isovic/gindex) registered for path 'codebase/gindex'
2018/01/30 19:10:59 ui: amazon-ebs: Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib.git) registered for path 'codebase/seqlib'
amazon-ebs: Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib.git) registered for path 'codebase/seqlib'
2018/01/30 19:10:59 ui: amazon-ebs: Cloning into 'codebase/argumentparser'...
amazon-ebs: Cloning into 'codebase/argumentparser'...
2018/01/30 19:11:00 ui: amazon-ebs: Submodule path 'codebase/argumentparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671'
amazon-ebs: Submodule path 'codebase/argumentparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671'
2018/01/30 19:11:00 ui: amazon-ebs: Cloning into 'codebase/gindex'...
amazon-ebs: Cloning into 'codebase/gindex'...
2018/01/30 19:11:00 ui: amazon-ebs: Submodule path 'codebase/gindex': checked out 'b1fb5ad35763632db66377348bb16fec29f381e4'
amazon-ebs: Submodule path 'codebase/gindex': checked out 'b1fb5ad35763632db66377348bb16fec29f381e4'
2018/01/30 19:11:00 ui: amazon-ebs: Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib) registered for path 'codebase/seqlib'
amazon-ebs: Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib) registered for path 'codebase/seqlib'
2018/01/30 19:11:00 ui: amazon-ebs: Cloning into 'codebase/seqlib'...
amazon-ebs: Cloning into 'codebase/seqlib'...
2018/01/30 19:11:01 ui: amazon-ebs: Submodule path 'codebase/gindex/codebase/seqlib': checked out 'bcfbcb1c77461c300d2ec0de03c0e1657a95cde2'
amazon-ebs: Submodule path 'codebase/gindex/codebase/seqlib': checked out 'bcfbcb1c77461c300d2ec0de03c0e1657a95cde2'
2018/01/30 19:11:01 ui: amazon-ebs: Cloning into 'codebase/seqlib'...
amazon-ebs: Cloning into 'codebase/seqlib'...
2018/01/30 19:11:01 ui: amazon-ebs: Submodule path 'codebase/seqlib': checked out 'd980be7a3cc0bc802eb910c10f084279f337992f'
amazon-ebs: Submodule path 'codebase/seqlib': checked out 'd980be7a3cc0bc802eb910c10f084279f337992f'
2018/01/30 19:11:01 ui: amazon-ebs: # git submodule foreach git pull origin master
amazon-ebs: # git submodule foreach git pull origin master
2018/01/30 19:11:01 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:01 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:01 ui: amazon-ebs: Makefile:100: "*** WARNING g++ minor version <7 ***"
amazon-ebs: Makefile:100: "*** WARNING g++ minor version <7 ***"
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/main.o codebase/gindex/src/main.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/argumentparser/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/main.o codebase/gindex/src/main.cc
amazon-ebs: mkdir -p obj_linux/codebase/argumentparser/src/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/argumentparser/src/example.o codebase/argumentparser/src/example.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/argumentparser/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/argumentparser/src/example.o codebase/argumentparser/src/example.cc
amazon-ebs: mkdir -p obj_linux/codebase/argumentparser/src/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.cc
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/experimental.o codebase/gindex/src/minimizer_index/experimental.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/experimental.o codebase/gindex/src/minimizer_index/experimental.cc
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o codebase/gindex/src/minimizer_index/compiled_shape.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o codebase/gindex/src/minimizer_index/compiled_shape.cc
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/seed.o codebase/gindex/src/minimizer_index/seed.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/seed.o codebase/gindex/src/minimizer_index/seed.cc
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o codebase/gindex/src/minimizer_index/minimizer_index.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o codebase/gindex/src/minimizer_index/minimizer_index.cc
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o codebase/gindex/src/minimizer_index/minimizer_generator.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o codebase/gindex/src/minimizer_index/minimizer_generator.cc
amazon-ebs: mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/index_pos.o codebase/gindex/src/minimizer_index/index_pos.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/gindex/src/minimizer_index/index_pos.o codebase/gindex/src/minimizer_index/index_pos.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:01 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
2018/01/30 19:11:01 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/log_system/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/log_system/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
amazon-ebs: mkdir -p obj_linux/src/alignment/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/alignment.o src/alignment/alignment.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/alignment.o src/alignment/alignment.cc
amazon-ebs: mkdir -p obj_linux/src/alignment/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/semiglobal.o src/alignment/semiglobal.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/semiglobal.o src/alignment/semiglobal.cc
amazon-ebs: mkdir -p obj_linux/src/alignment/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/cigargen.o src/alignment/cigargen.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/cigargen.o src/alignment/cigargen.cc
amazon-ebs: mkdir -p obj_linux/src/alignment/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/transcriptome_mod.o src/alignment/transcriptome_mod.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/transcriptome_mod.o src/alignment/transcriptome_mod.cc
amazon-ebs: mkdir -p obj_linux/src/alignment/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/anchored.o src/alignment/anchored.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/anchored.o src/alignment/anchored.cc
amazon-ebs: mkdir -p obj_linux/src/alignment/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
amazon-ebs: mkdir -p obj_linux/src/index/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/index/index_util.o src/index/index_util.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/index/index_util.o src/index/index_util.cc
amazon-ebs: mkdir -p obj_linux/src/containers/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/path_graph_entry.o src/containers/path_graph_entry.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/path_graph_entry.o src/containers/path_graph_entry.cc
amazon-ebs: mkdir -p obj_linux/src/containers/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/mapping_data.o src/containers/mapping_data.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/mapping_data.o src/containers/mapping_data.cc
amazon-ebs: mkdir -p obj_linux/src/containers/
2018/01/30 19:11:02 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/vertices.o src/containers/vertices.cc
2018/01/30 19:11:02 ui: amazon-ebs: mkdir -p obj_linux/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/vertices.o src/containers/vertices.cc
amazon-ebs: mkdir -p obj_linux/src/containers/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/region.o src/containers/region.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/region.o src/containers/region.cc
amazon-ebs: mkdir -p obj_linux/src/containers/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/score_registry.o src/containers/score_registry.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/containers/score_registry.o src/containers/score_registry.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/experimental.o src/graphmap/experimental.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/experimental.o src/graphmap/experimental.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/lcs_anchored.o src/graphmap/lcs_anchored.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/lcs_anchored.o src/graphmap/lcs_anchored.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/region_selection.o src/graphmap/region_selection.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/region_selection.o src/graphmap/region_selection.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/process_read.o src/graphmap/process_read.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/process_read.o src/graphmap/process_read.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/transcriptome.o src/graphmap/transcriptome.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/transcriptome.o src/graphmap/transcriptome.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/lcs_semiglobal.o src/graphmap/lcs_semiglobal.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/lcs_semiglobal.o src/graphmap/lcs_semiglobal.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/filter_anchors.o src/graphmap/filter_anchors.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/filter_anchors.o src/graphmap/filter_anchors.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/graphmap.o src/graphmap/graphmap.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/graphmap.o src/graphmap/graphmap.cc
amazon-ebs: mkdir -p obj_linux/src/graphmap/
2018/01/30 19:11:03 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/core_graphmap.o src/graphmap/core_graphmap.cc
2018/01/30 19:11:03 ui: amazon-ebs: mkdir -p obj_linux/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/graphmap/core_graphmap.o src/graphmap/core_graphmap.cc
amazon-ebs: mkdir -p obj_linux/src/owler/
2018/01/30 19:11:04 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/owler.o src/owler/owler.cc
2018/01/30 19:11:04 ui: amazon-ebs: mkdir -p obj_linux/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/owler.o src/owler/owler.cc
amazon-ebs: mkdir -p obj_linux/src/owler/
2018/01/30 19:11:04 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/lcsk.o src/owler/lcsk.cc
2018/01/30 19:11:04 ui: amazon-ebs: mkdir -p obj_linux/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/lcsk.o src/owler/lcsk.cc
amazon-ebs: mkdir -p obj_linux/src/owler/
2018/01/30 19:11:04 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/process_read.o src/owler/process_read.cc
2018/01/30 19:11:04 ui: amazon-ebs: mkdir -p obj_linux/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/process_read.o src/owler/process_read.cc
amazon-ebs: mkdir -p obj_linux/src/owler/
2018/01/30 19:11:04 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/owler_experimental.o src/owler/owler_experimental.cc
2018/01/30 19:11:04 ui: amazon-ebs: mkdir -p obj_linux/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/owler_experimental.o src/owler/owler_experimental.cc
amazon-ebs: mkdir -p obj_linux/src/
2018/01/30 19:11:04 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/program_parameters.o src/program_parameters.cc
2018/01/30 19:11:04 ui: amazon-ebs: mkdir -p obj_linux/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/program_parameters.o src/program_parameters.cc
amazon-ebs: mkdir -p obj_linux/src/
2018/01/30 19:11:04 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/main.o src/main.cc
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/main.o src/main.cc
^[[A2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p ./bin/Linux-x64/
amazon-ebs: mkdir -p ./bin/Linux-x64/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/src/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/index/index_util.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/transcriptome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/program_parameters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz
amazon-ebs: g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/src/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/index/index_util.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/transcriptome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/program_parameters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz
2018/01/30 19:11:14 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/isovic/graphmap.git; cd graphmap && make modules && make -j testing
amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/isovic/graphmap.git; cd graphmap && make modules && make -j testing
2018/01/30 19:11:14 ui: amazon-ebs: fatal: destination path 'graphmap' already exists and is not an empty directory.
amazon-ebs: fatal: destination path 'graphmap' already exists and is not an empty directory.
2018/01/30 19:11:14 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:14 ui: amazon-ebs: git submodule update --init --recursive
amazon-ebs: git submodule update --init --recursive
2018/01/30 19:11:14 ui: amazon-ebs: # git submodule foreach git pull origin master
amazon-ebs: # git submodule foreach git pull origin master
2018/01/30 19:11:14 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:14 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/main.o codebase/gindex/src/main.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/argumentparser/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/main.o codebase/gindex/src/main.cc
amazon-ebs: mkdir -p obj_test/codebase/argumentparser/src/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/argumentparser/src/example.o codebase/argumentparser/src/example.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/argumentparser/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/argumentparser/src/example.o codebase/argumentparser/src/example.cc
amazon-ebs: mkdir -p obj_test/codebase/argumentparser/src/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.cc
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/experimental.o codebase/gindex/src/minimizer_index/experimental.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/experimental.o codebase/gindex/src/minimizer_index/experimental.cc
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/compiled_shape.o codebase/gindex/src/minimizer_index/compiled_shape.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/compiled_shape.o codebase/gindex/src/minimizer_index/compiled_shape.cc
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/seed.o codebase/gindex/src/minimizer_index/seed.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/seed.o codebase/gindex/src/minimizer_index/seed.cc
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/minimizer_index.o codebase/gindex/src/minimizer_index/minimizer_index.cc
2018/01/30 19:11:14 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/minimizer_index.o codebase/gindex/src/minimizer_index/minimizer_index.cc
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:14 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/minimizer_generator.o codebase/gindex/src/minimizer_index/minimizer_generator.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/minimizer_generator.o codebase/gindex/src/minimizer_index/minimizer_generator.cc
amazon-ebs: mkdir -p obj_test/codebase/gindex/src/minimizer_index/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/index_pos.o codebase/gindex/src/minimizer_index/index_pos.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/gindex/src/minimizer_index/index_pos.o codebase/gindex/src/minimizer_index/index_pos.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/utility/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/sequences/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/log_system/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/log_system/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
amazon-ebs: mkdir -p obj_test/codebase/seqlib/src/libs/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
amazon-ebs: mkdir -p obj_test/src/alignment/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/alignment.o src/alignment/alignment.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/alignment.o src/alignment/alignment.cc
amazon-ebs: mkdir -p obj_test/src/alignment/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/semiglobal.o src/alignment/semiglobal.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/semiglobal.o src/alignment/semiglobal.cc
amazon-ebs: mkdir -p obj_test/src/alignment/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/cigargen.o src/alignment/cigargen.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/cigargen.o src/alignment/cigargen.cc
amazon-ebs: mkdir -p obj_test/src/alignment/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/transcriptome_mod.o src/alignment/transcriptome_mod.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/transcriptome_mod.o src/alignment/transcriptome_mod.cc
amazon-ebs: mkdir -p obj_test/src/alignment/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/anchored.o src/alignment/anchored.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/alignment/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/anchored.o src/alignment/anchored.cc
amazon-ebs: mkdir -p obj_test/src/alignment/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/index/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
amazon-ebs: mkdir -p obj_test/src/index/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/index/index_util.o src/index/index_util.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/index/index_util.o src/index/index_util.cc
amazon-ebs: mkdir -p obj_test/src/containers/
2018/01/30 19:11:15 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/path_graph_entry.o src/containers/path_graph_entry.cc
2018/01/30 19:11:15 ui: amazon-ebs: mkdir -p obj_test/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/path_graph_entry.o src/containers/path_graph_entry.cc
amazon-ebs: mkdir -p obj_test/src/containers/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/mapping_data.o src/containers/mapping_data.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/mapping_data.o src/containers/mapping_data.cc
amazon-ebs: mkdir -p obj_test/src/containers/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/vertices.o src/containers/vertices.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/vertices.o src/containers/vertices.cc
amazon-ebs: mkdir -p obj_test/src/containers/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/region.o src/containers/region.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/containers/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/region.o src/containers/region.cc
amazon-ebs: mkdir -p obj_test/src/containers/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/score_registry.o src/containers/score_registry.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/containers/score_registry.o src/containers/score_registry.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/experimental.o src/graphmap/experimental.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/experimental.o src/graphmap/experimental.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/lcs_anchored.o src/graphmap/lcs_anchored.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/lcs_anchored.o src/graphmap/lcs_anchored.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/region_selection.o src/graphmap/region_selection.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/region_selection.o src/graphmap/region_selection.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/process_read.o src/graphmap/process_read.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/process_read.o src/graphmap/process_read.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/transcriptome.o src/graphmap/transcriptome.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/transcriptome.o src/graphmap/transcriptome.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/lcs_semiglobal.o src/graphmap/lcs_semiglobal.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/lcs_semiglobal.o src/graphmap/lcs_semiglobal.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:16 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/filter_anchors.o src/graphmap/filter_anchors.cc
2018/01/30 19:11:16 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/filter_anchors.o src/graphmap/filter_anchors.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/graphmap.o src/graphmap/graphmap.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/graphmap/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/graphmap.o src/graphmap/graphmap.cc
amazon-ebs: mkdir -p obj_test/src/graphmap/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/core_graphmap.o src/graphmap/core_graphmap.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/graphmap/core_graphmap.o src/graphmap/core_graphmap.cc
amazon-ebs: mkdir -p obj_test/src/owler/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/owler.o src/owler/owler.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/owler.o src/owler/owler.cc
amazon-ebs: mkdir -p obj_test/src/owler/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/lcsk.o src/owler/lcsk.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/lcsk.o src/owler/lcsk.cc
amazon-ebs: mkdir -p obj_test/src/owler/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/process_read.o src/owler/process_read.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/owler/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/process_read.o src/owler/process_read.cc
amazon-ebs: mkdir -p obj_test/src/owler/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/owler_experimental.o src/owler/owler_experimental.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/owler/owler_experimental.o src/owler/owler_experimental.cc
amazon-ebs: mkdir -p obj_test/src/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/program_parameters.o src/program_parameters.cc
2018/01/30 19:11:17 ui: amazon-ebs: mkdir -p obj_test/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/program_parameters.o src/program_parameters.cc
amazon-ebs: mkdir -p obj_test/src/
2018/01/30 19:11:17 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/main.o src/main.cc
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/seqlib/src -Icodebase/gindex/src -Icodebase/argumentparser/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/main.o src/main.cc
2018/01/30 19:11:28 ui: amazon-ebs: mkdir -p ./bin/
amazon-ebs: mkdir -p ./bin/
2018/01/30 19:11:28 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/graphmap-not_release ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_test/codebase/gindex/src/main.o ./obj_test/codebase/argumentparser/src/example.o ./obj_test/codebase/argumentparser/src/argparser.o ./obj_test/codebase/seqlib/src/test.o ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_test/codebase/gindex/src/minimizer_index/experimental.o ./obj_test/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_test/codebase/gindex/src/minimizer_index/seed.o ./obj_test/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_test/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_test/codebase/gindex/src/minimizer_index/index_pos.o ./obj_test/codebase/seqlib/src/utility/utility_general.o ./obj_test/codebase/seqlib/src/utility/tictoc.o ./obj_test/codebase/seqlib/src/utility/evalue.o ./obj_test/codebase/seqlib/src/utility/evalue_constants.o ./obj_test/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_test/codebase/seqlib/src/sequences/sequence_file.o ./obj_test/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_test/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_test/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_test/codebase/seqlib/src/sequences/single_sequence.o ./obj_test/codebase/seqlib/src/log_system/log_system.o ./obj_test/codebase/seqlib/src/libs/edlib.o ./obj_test/codebase/seqlib/src/libs/edlibcigar.o ./obj_test/codebase/seqlib/src/libs/opal.o ./obj_test/src/alignment/alignment.o ./obj_test/src/alignment/semiglobal.o ./obj_test/src/alignment/cigargen.o ./obj_test/src/alignment/transcriptome_mod.o ./obj_test/src/alignment/anchored.o ./obj_test/src/alignment/alignment_wrappers.o ./obj_test/src/index/index_util.o ./obj_test/src/containers/path_graph_entry.o ./obj_test/src/containers/mapping_data.o ./obj_test/src/containers/vertices.o ./obj_test/src/containers/region.o ./obj_test/src/containers/score_registry.o ./obj_test/src/graphmap/experimental.o ./obj_test/src/graphmap/lcs_anchored.o ./obj_test/src/graphmap/region_selection.o ./obj_test/src/graphmap/process_read.o ./obj_test/src/graphmap/transcriptome.o ./obj_test/src/graphmap/lcs_semiglobal.o ./obj_test/src/graphmap/filter_anchors.o ./obj_test/src/graphmap/graphmap.o ./obj_test/src/graphmap/core_graphmap.o ./obj_test/src/owler/owler.o ./obj_test/src/owler/lcsk.o ./obj_test/src/owler/process_read.o ./obj_test/src/owler/owler_experimental.o ./obj_test/src/program_parameters.o ./obj_test/src/main.o -lpthread -lgomp -lm -lz
amazon-ebs: g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/graphmap-not_release ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_test/codebase/gindex/src/main.o ./obj_test/codebase/argumentparser/src/example.o ./obj_test/codebase/argumentparser/src/argparser.o ./obj_test/codebase/seqlib/src/test.o ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_test/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_test/codebase/gindex/src/minimizer_index/experimental.o ./obj_test/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_test/codebase/gindex/src/minimizer_index/seed.o ./obj_test/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_test/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_test/codebase/gindex/src/minimizer_index/index_pos.o ./obj_test/codebase/seqlib/src/utility/utility_general.o ./obj_test/codebase/seqlib/src/utility/tictoc.o ./obj_test/codebase/seqlib/src/utility/evalue.o ./obj_test/codebase/seqlib/src/utility/evalue_constants.o ./obj_test/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_test/codebase/seqlib/src/sequences/sequence_file.o ./obj_test/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_test/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_test/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_test/codebase/seqlib/src/sequences/single_sequence.o ./obj_test/codebase/seqlib/src/log_system/log_system.o ./obj_test/codebase/seqlib/src/libs/edlib.o ./obj_test/codebase/seqlib/src/libs/edlibcigar.o ./obj_test/codebase/seqlib/src/libs/opal.o ./obj_test/src/alignment/alignment.o ./obj_test/src/alignment/semiglobal.o ./obj_test/src/alignment/cigargen.o ./obj_test/src/alignment/transcriptome_mod.o ./obj_test/src/alignment/anchored.o ./obj_test/src/alignment/alignment_wrappers.o ./obj_test/src/index/index_util.o ./obj_test/src/containers/path_graph_entry.o ./obj_test/src/containers/mapping_data.o ./obj_test/src/containers/vertices.o ./obj_test/src/containers/region.o ./obj_test/src/containers/score_registry.o ./obj_test/src/graphmap/experimental.o ./obj_test/src/graphmap/lcs_anchored.o ./obj_test/src/graphmap/region_selection.o ./obj_test/src/graphmap/process_read.o ./obj_test/src/graphmap/transcriptome.o ./obj_test/src/graphmap/lcs_semiglobal.o ./obj_test/src/graphmap/filter_anchors.o ./obj_test/src/graphmap/graphmap.o ./obj_test/src/graphmap/core_graphmap.o ./obj_test/src/owler/owler.o ./obj_test/src/owler/lcsk.o ./obj_test/src/owler/process_read.o ./obj_test/src/owler/owler_experimental.o ./obj_test/src/program_parameters.o ./obj_test/src/main.o -lpthread -lgomp -lm -lz
2018/01/30 19:11:28 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/graphmap'
2018/01/30 19:11:28 ui: amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/isovic/edlib.git; cd edlib; cd src && make -j
amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/isovic/edlib.git; cd edlib; cd src && make -j
2018/01/30 19:11:28 ui: amazon-ebs: Cloning into 'edlib'...
amazon-ebs: Cloning into 'edlib'...
2018/01/30 19:11:28 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/edlib/src'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/edlib/src'
2018/01/30 19:11:28 ui: amazon-ebs: g++ -O3 -c edlib.cpp
amazon-ebs: g++ -O3 -c edlib.cpp
2018/01/30 19:11:29 ui: amazon-ebs: g++ -O3 edlib.o test.cpp -o test
amazon-ebs: g++ -O3 edlib.o test.cpp -o test
2018/01/30 19:11:29 ui: amazon-ebs: g++ -O3 edlib.o aligner.cpp -o aligner
amazon-ebs: g++ -O3 edlib.o aligner.cpp -o aligner
2018/01/30 19:11:29 ui: amazon-ebs: g++ -O3 edlib.o kmercomp.cpp -o kmercomp
amazon-ebs: g++ -O3 edlib.o kmercomp.cpp -o kmercomp
2018/01/30 19:11:29 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/edlib/src'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/edlib/src'
2018/01/30 19:11:29 ui: amazon-ebs: # mkdir -p tools; cd tools; git clone https://github.com/Martinsos/edlib.git; cd edlib; git checkout 06d8e77f6ec5efb43aa04109caf53e9868695c75; cd src && make -j
amazon-ebs: # mkdir -p tools; cd tools; git clone https://github.com/Martinsos/edlib.git; cd edlib; git checkout 06d8e77f6ec5efb43aa04109caf53e9868695c75; cd src && make -j
2018/01/30 19:11:29 ui: amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/lh3/minimap.git; cd minimap; make -j
amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/lh3/minimap.git; cd minimap; make -j
2018/01/30 19:11:29 ui: amazon-ebs: Cloning into 'minimap'...
amazon-ebs: Cloning into 'minimap'...
2018/01/30 19:11:30 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/minimap'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/minimap'
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial main.c -o main.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial main.c -o main.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial kthread.c -o kthread.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial kthread.c -o kthread.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial misc.c -o misc.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial misc.c -o misc.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial bseq.c -o bseq.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial bseq.c -o bseq.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial sketch.c -o sketch.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial sketch.c -o sketch.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial sdust.c -o sdust.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial sdust.c -o sdust.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial index.c -o index.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial index.c -o index.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial map.c -o map.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -Wno-unused-function -I/usr/include/hdf5/serial map.c -o map.o
2018/01/30 19:11:30 ui: amazon-ebs: index.c: In function ‘mm_idx_load’:
amazon-ebs: index.c: In function ‘mm_idx_load’:
2018/01/30 19:11:30 ui: amazon-ebs: index.c:317:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:317:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(&mi->freq_thres, sizeof(float), 1, fp);
amazon-ebs: fread(&mi->freq_thres, sizeof(float), 1, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:319:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:319:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(mi->len, 4, mi->n, fp);
amazon-ebs: fread(mi->len, 4, mi->n, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:324:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:324:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(&l, 1, 1, fp);
amazon-ebs: fread(&l, 1, 1, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:326:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:326:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(mi->name[i], 1, l, fp);
amazon-ebs: fread(mi->name[i], 1, l, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:335:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:335:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(&b->n, 4, 1, fp);
amazon-ebs: fread(&b->n, 4, 1, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:337:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:337:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(b->p, 8, b->n, fp);
amazon-ebs: fread(b->p, 8, b->n, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:338:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:338:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(&size, 4, 1, fp);
amazon-ebs: fread(&size, 4, 1, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: index.c:345:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
amazon-ebs: index.c:345:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
2018/01/30 19:11:30 ui: amazon-ebs: fread(x, 8, 2, fp);
amazon-ebs: fread(x, 8, 2, fp);
2018/01/30 19:11:30 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:30 ui: amazon-ebs: ar -csru libminimap.a kthread.o misc.o bseq.o sketch.o sdust.o index.o map.o
amazon-ebs: ar -csru libminimap.a kthread.o misc.o bseq.o sketch.o sdust.o index.o map.o
2018/01/30 19:11:30 ui: amazon-ebs: ar: `u' modifier ignored since `D' is the default (see `U')
amazon-ebs: ar: `u' modifier ignored since `D' is the default (see `U')
2018/01/30 19:11:30 ui: amazon-ebs: gcc -g -Wall -O2 -Wc++-compat -Wno-unused-function main.o -o minimap -L. -lminimap -lm -lz -lpthread
amazon-ebs: gcc -g -Wall -O2 -Wc++-compat -Wno-unused-function main.o -o minimap -L. -lminimap -lm -lz -lpthread
2018/01/30 19:11:30 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/minimap'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/minimap'
2018/01/30 19:11:30 ui: amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/lh3/miniasm.git; cd miniasm; make -j
amazon-ebs: mkdir -p tools; cd tools; git clone https://github.com/lh3/miniasm.git; cd miniasm; make -j
2018/01/30 19:11:30 ui: amazon-ebs: Cloning into 'miniasm'...
amazon-ebs: Cloning into 'miniasm'...
2018/01/30 19:11:30 ui: amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/miniasm'
amazon-ebs: make[2]: Entering directory '/home/ubuntu/pomoxis/submodules/racon/tools/miniasm'
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sys.c -o sys.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sys.c -o sys.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sdict.c -o sdict.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. sdict.c -o sdict.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. paf.c -o paf.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. paf.c -o paf.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asg.c -o asg.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asg.c -o asg.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. common.c -o common.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. common.c -o common.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. hit.c -o hit.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. hit.c -o hit.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asm.c -o asm.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. asm.c -o asm.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. main.c -o main.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. main.c -o main.o
2018/01/30 19:11:30 ui: amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. dotter.c -o dotter.o
amazon-ebs: gcc -c -g -Wall -O2 -Wc++-compat -I. dotter.c -o dotter.o
2018/01/30 19:11:31 ui: amazon-ebs: gcc -g -Wall -O2 -Wc++-compat sys.o sdict.o paf.o asg.o common.o hit.o asm.o main.o -o miniasm -lm -lz -lpthread
amazon-ebs: gcc -g -Wall -O2 -Wc++-compat sys.o sdict.o paf.o asg.o common.o hit.o asm.o main.o -o miniasm -lm -lz -lpthread
2018/01/30 19:11:31 ui: amazon-ebs: gcc -g -Wall -O2 -Wc++-compat paf.o sdict.o dotter.o -o minidot -lm -lz -lpthread
amazon-ebs: gcc -g -Wall -O2 -Wc++-compat paf.o sdict.o dotter.o -o minidot -lm -lz -lpthread
2018/01/30 19:11:31 ui: amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/miniasm'
amazon-ebs: make[2]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon/tools/miniasm'
2018/01/30 19:11:31 ui: amazon-ebs: echo "All tools installed."
amazon-ebs: echo "All tools installed."
2018/01/30 19:11:31 ui: amazon-ebs: All tools installed.
amazon-ebs: All tools installed.
2018/01/30 19:11:31 ui: amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon'
amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon'
2018/01/30 19:11:31 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/racon'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/racon'
2018/01/30 19:11:31 ui: amazon-ebs: Makefile:81: "*** WARNING g++ minor version <7 ***"
amazon-ebs: Makefile:81: "*** WARNING g++ minor version <7 ***"
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/sisd_alignment.o codebase/spoa/src/sisd_alignment.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/sisd_alignment.o codebase/spoa/src/sisd_alignment.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/edge.o codebase/spoa/src/edge.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/edge.o codebase/spoa/src/edge.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/simd_alignment.o codebase/spoa/src/simd_alignment.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/simd_alignment.o codebase/spoa/src/simd_alignment.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/alignment.o codebase/spoa/src/alignment.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/alignment.o codebase/spoa/src/alignment.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/node.o codebase/spoa/src/node.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/node.o codebase/spoa/src/node.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/graph.o codebase/spoa/src/graph.cpp
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/graph.o codebase/spoa/src/graph.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/main.o codebase/spoa/src/main.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/main.o codebase/spoa/src/main.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/spoa.o codebase/spoa/src/spoa.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/spoa.o codebase/spoa/src/spoa.cpp
amazon-ebs: mkdir -p obj_linux/codebase/spoa/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/chain.o codebase/spoa/src/chain.cpp
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/argparser/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/spoa/src/chain.o codebase/spoa/src/chain.cpp
amazon-ebs: mkdir -p obj_linux/codebase/argparser/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/argparser/src/example.o codebase/argparser/src/example.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/argparser/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/argparser/src/example.o codebase/argparser/src/example.cc
amazon-ebs: mkdir -p obj_linux/codebase/argparser/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/argparser/src/argparser.o codebase/argparser/src/argparser.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/argparser/src/argparser.o codebase/argparser/src/argparser.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/utility/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/sequences/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/log_system/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/log_system/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
amazon-ebs: mkdir -p obj_linux/codebase/seqlib/src/libs/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/src/consensus/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
amazon-ebs: mkdir -p obj_linux/src/consensus/
2018/01/30 19:11:31 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/pileup.o src/consensus/pileup.cc
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/pileup.o src/consensus/pileup.cc
2018/01/30 19:11:31 ui: amazon-ebs: mkdir -p obj_linux/src/consensus/
amazon-ebs: mkdir -p obj_linux/src/consensus/
2018/01/30 19:11:32 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/tictoc.o src/consensus/tictoc.cc
2018/01/30 19:11:32 ui: amazon-ebs: mkdir -p obj_linux/src/consensus/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/tictoc.o src/consensus/tictoc.cc
amazon-ebs: mkdir -p obj_linux/src/consensus/
2018/01/30 19:11:32 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/consensus_sam.o src/consensus/consensus_sam.cc
2018/01/30 19:11:32 ui: amazon-ebs: mkdir -p obj_linux/src/consensus/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/consensus_sam.o src/consensus/consensus_sam.cc
amazon-ebs: mkdir -p obj_linux/src/consensus/
2018/01/30 19:11:32 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/consensus_overlap.o src/consensus/consensus_overlap.cc
2018/01/30 19:11:32 ui: amazon-ebs: mkdir -p obj_linux/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/consensus/consensus_overlap.o src/consensus/consensus_overlap.cc
amazon-ebs: mkdir -p obj_linux/src/
2018/01/30 19:11:32 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/main.o src/main.cc
2018/01/30 19:11:32 ui: amazon-ebs: mkdir -p obj_linux/src/
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/main.o src/main.cc
amazon-ebs: mkdir -p obj_linux/src/
2018/01/30 19:11:32 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/mhap.o src/mhap.cc
amazon-ebs: g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -Icodebase/seqlib/src -Icodebase/samscripts/src -Icodebase/argparser/src -Icodebase/spoa/src -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -march=native -o obj_linux/src/mhap.o src/mhap.cc
2018/01/30 19:11:35 ui: amazon-ebs: mkdir -p ./bin/
amazon-ebs: mkdir -p ./bin/
2018/01/30 19:11:35 ui: amazon-ebs: g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/racon ./obj_linux/codebase/spoa/src/sisd_alignment.o ./obj_linux/codebase/spoa/src/edge.o ./obj_linux/codebase/spoa/src/simd_alignment.o ./obj_linux/codebase/spoa/src/alignment.o ./obj_linux/codebase/spoa/src/node.o ./obj_linux/codebase/spoa/src/graph.o ./obj_linux/codebase/spoa/src/main.o ./obj_linux/codebase/spoa/src/spoa.o ./obj_linux/codebase/spoa/src/chain.o ./obj_linux/codebase/argparser/src/example.o ./obj_linux/codebase/argparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/consensus/pileup.o ./obj_linux/src/consensus/tictoc.o ./obj_linux/src/consensus/consensus_sam.o ./obj_linux/src/consensus/consensus_overlap.o ./obj_linux/src/main.o ./obj_linux/src/mhap.o -lpthread -lgomp -lm -lz
amazon-ebs: g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/racon ./obj_linux/codebase/spoa/src/sisd_alignment.o ./obj_linux/codebase/spoa/src/edge.o ./obj_linux/codebase/spoa/src/simd_alignment.o ./obj_linux/codebase/spoa/src/alignment.o ./obj_linux/codebase/spoa/src/node.o ./obj_linux/codebase/spoa/src/graph.o ./obj_linux/codebase/spoa/src/main.o ./obj_linux/codebase/spoa/src/spoa.o ./obj_linux/codebase/spoa/src/chain.o ./obj_linux/codebase/argparser/src/example.o ./obj_linux/codebase/argparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/consensus/pileup.o ./obj_linux/src/consensus/tictoc.o ./obj_linux/src/consensus/consensus_sam.o ./obj_linux/src/consensus/consensus_overlap.o ./obj_linux/src/main.o ./obj_linux/src/mhap.o -lpthread -lgomp -lm -lz
2018/01/30 19:11:36 ui: amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon'
amazon-ebs: make[1]: Leaving directory '/home/ubuntu/pomoxis/submodules/racon'
2018/01/30 19:11:36 ui: amazon-ebs: cp submodules/racon/bin/racon bincache/racon
amazon-ebs: cp submodules/racon/bin/racon bincache/racon
2018/01/30 19:11:36 ui: amazon-ebs: Making samtools
amazon-ebs: Making samtools
2018/01/30 19:11:36 ui: amazon-ebs: # tar.bz is not a dependency, since that would cause it to be fetched
amazon-ebs: # tar.bz is not a dependency, since that would cause it to be fetched
2018/01/30 19:11:36 ui: amazon-ebs: # even when installing from bincache
amazon-ebs: # even when installing from bincache
2018/01/30 19:11:36 ui: amazon-ebs: if [ ! -e submodules/samtools-1.3.1.tar.bz2 ]; then \
amazon-ebs: if [ ! -e submodules/samtools-1.3.1.tar.bz2 ]; then \
2018/01/30 19:11:36 ui: amazon-ebs: cd submodules; \
amazon-ebs: cd submodules; \
2018/01/30 19:11:36 ui: amazon-ebs: wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2; \
amazon-ebs: wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2; \
2018/01/30 19:11:36 ui: amazon-ebs: --2018-01-31 03:11:36-- https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
amazon-ebs: --2018-01-31 03:11:36-- https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
2018/01/30 19:11:36 ui: amazon-ebs: fi
amazon-ebs: fi
2018/01/30 19:11:36 ui: amazon-ebs: Resolving github.com (github.com)... 192.30.255.112, 192.30.255.113
amazon-ebs: Resolving github.com (github.com)... 192.30.255.112, 192.30.255.113
2018/01/30 19:11:36 ui: amazon-ebs: Connecting to github.com (github.com)|192.30.255.112|:443... connected.
amazon-ebs: Connecting to github.com (github.com)|192.30.255.112|:443... connected.
2018/01/30 19:11:36 ui: amazon-ebs: HTTP request sent, awaiting response... 302 Found
amazon-ebs: HTTP request sent, awaiting response... 302 Found
2018/01/30 19:11:36 ui: amazon-ebs: Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/3666841/94dfe70a-0895-11e6-8856-070f81e24fde?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180131%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180131T031136Z&X-Amz-Expires=300&X-Amz-Signature=5e1b98c5c67b940681011453376904100567b192cf71f4af1a2ce57e2e6aad39&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dsamtools-1.3.1.tar.bz2&response-content-type=application%2Foctet-stream [following]
2018/01/30 19:11:36 ui: amazon-ebs: --2018-01-31 03:11:36-- https://github-production-release-asset-2e65be.s3.amazonaws.com/3666841/94dfe70a-0895-11e6-8856-070f81e24fde?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180131%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180131T031136Z&X-Amz-Expires=300&X-Amz-Signature=5e1b98c5c67b940681011453376904100567b192cf71f4af1a2ce57e2e6aad39&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dsamtools-1.3.1.tar.bz2&response-content-type=application%2Foctet-stream
amazon-ebs: Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/3666841/94dfe70a-0895-11e6-8856-070f81e24fde?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180131%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180131T031136Z&X-Amz-Expires=300&X-Amz-Signature=5e1b98c5c67b940681011453376904100567b192cf71f4af1a2ce57e2e6aad39&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dsamtools-1.3.1.tar.bz2&response-content-type=application%2Foctet-stream [following]
amazon-ebs: --2018-01-31 03:11:36-- https://github-production-release-asset-2e65be.s3.amazonaws.com/3666841/94dfe70a-0895-11e6-8856-070f81e24fde?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180131%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180131T031136Z&X-Amz-Expires=300&X-Amz-Signature=5e1b98c5c67b940681011453376904100567b192cf71f4af1a2ce57e2e6aad39&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dsamtools-1.3.1.tar.bz2&response-content-type=application%2Foctet-stream
2018/01/30 19:11:36 ui: amazon-ebs: Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.18.88
amazon-ebs: Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.18.88
2018/01/30 19:11:36 ui: amazon-ebs: Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.18.88|:443... connected.
amazon-ebs: Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.18.88|:443... connected.
2018/01/30 19:11:36 ui: amazon-ebs: HTTP request sent, awaiting response... 200 OK
amazon-ebs: HTTP request sent, awaiting response... 200 OK
2018/01/30 19:11:36 ui: amazon-ebs: Length: 4030072 (3.8M) [application/octet-stream]
amazon-ebs: Length: 4030072 (3.8M) [application/octet-stream]
2018/01/30 19:11:36 ui: amazon-ebs: Saving to: ‘samtools-1.3.1.tar.bz2’
amazon-ebs: Saving to: ‘samtools-1.3.1.tar.bz2’
2018/01/30 19:11:36 ui: amazon-ebs:
amazon-ebs:
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amazon-ebs: 0K .......... .......... .......... .......... .......... 1% 248K 16s
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amazon-ebs: 3750K .......... .......... .......... .......... .......... 96% 189M 0s
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2018/01/30 19:11:38 ui: amazon-ebs: 3900K .......... .......... .......... ..... 100% 90.2M=1.9s
amazon-ebs: 3900K .......... .......... .......... ..... 100% 90.2M=1.9s
2018/01/30 19:11:38 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:11:38 ui: amazon-ebs: 2018-01-31 03:11:38 (2.07 MB/s) - ‘samtools-1.3.1.tar.bz2’ saved [4030072/4030072]
amazon-ebs: 2018-01-31 03:11:38 (2.07 MB/s) - ‘samtools-1.3.1.tar.bz2’ saved [4030072/4030072]
2018/01/30 19:11:38 ui: amazon-ebs:
amazon-ebs:
2018/01/30 19:11:38 ui: amazon-ebs: cd submodules && tar -xjf samtools-1.3.1.tar.bz2
amazon-ebs: cd submodules && tar -xjf samtools-1.3.1.tar.bz2
2018/01/30 19:11:39 ui: amazon-ebs: cd submodules/samtools-1.3.1 && make
amazon-ebs: cd submodules/samtools-1.3.1 && make
2018/01/30 19:11:39 ui: amazon-ebs: Makefile:98: config.mk: No such file or directory
amazon-ebs: Makefile:98: config.mk: No such file or directory
2018/01/30 19:11:39 ui: amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/samtools-1.3.1'
amazon-ebs: make[1]: Entering directory '/home/ubuntu/pomoxis/submodules/samtools-1.3.1'
2018/01/30 19:11:39 ui: amazon-ebs: echo '/* Basic config.h generated by Makefile */' > config.h
amazon-ebs: echo '/* Basic config.h generated by Makefile */' > config.h
2018/01/30 19:11:39 ui: amazon-ebs: echo '#define HAVE_CURSES' >> config.h
amazon-ebs: echo '#define HAVE_CURSES' >> config.h
2018/01/30 19:11:39 ui: amazon-ebs: echo '#define HAVE_CURSES_H' >> config.h
amazon-ebs: echo '#define HAVE_CURSES_H' >> config.h
2018/01/30 19:11:39 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_index.o bam_index.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_index.o bam_index.c
2018/01/30 19:11:39 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_plcmd.o bam_plcmd.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_plcmd.o bam_plcmd.c
2018/01/30 19:11:39 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o sam_view.o sam_view.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o sam_view.o sam_view.c
2018/01/30 19:11:40 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_cat.o bam_cat.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_cat.o bam_cat.c
2018/01/30 19:11:40 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_md.o bam_md.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_md.o bam_md.c
2018/01/30 19:11:41 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_reheader.o bam_reheader.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_reheader.o bam_reheader.c
2018/01/30 19:11:41 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_sort.o bam_sort.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_sort.o bam_sort.c
2018/01/30 19:11:42 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bedidx.o bedidx.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bedidx.o bedidx.c
2018/01/30 19:11:43 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o kprobaln.o kprobaln.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o kprobaln.o kprobaln.c
2018/01/30 19:11:43 ui: amazon-ebs: kprobaln.c: In function ‘kpa_glocal’:
amazon-ebs: kprobaln.c: In function ‘kpa_glocal’:
2018/01/30 19:11:43 ui: amazon-ebs: kprobaln.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
amazon-ebs: kprobaln.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
2018/01/30 19:11:43 ui: amazon-ebs: int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
amazon-ebs: int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
2018/01/30 19:11:43 ui: amazon-ebs: ^
amazon-ebs: ^
2018/01/30 19:11:43 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_rmdup.o bam_rmdup.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_rmdup.o bam_rmdup.c
2018/01/30 19:11:44 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_rmdupse.o bam_rmdupse.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_rmdupse.o bam_rmdupse.c
2018/01/30 19:11:44 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_mate.o bam_mate.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_mate.o bam_mate.c
2018/01/30 19:11:44 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_stat.o bam_stat.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_stat.o bam_stat.c
2018/01/30 19:11:44 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_color.o bam_color.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam_color.o bam_color.c
2018/01/30 19:11:44 ui: amazon-ebs: echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
amazon-ebs: echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
2018/01/30 19:11:44 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bamtk.o bamtk.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bamtk.o bamtk.c
2018/01/30 19:11:44 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam2bcf.o bam2bcf.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam2bcf.o bam2bcf.c
2018/01/30 19:11:45 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam2bcf_indel.o bam2bcf_indel.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam2bcf_indel.o bam2bcf_indel.c
2018/01/30 19:11:45 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o errmod.o errmod.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o errmod.o errmod.c
2018/01/30 19:11:46 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o sample.o sample.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o sample.o sample.c
2018/01/30 19:11:46 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o sam_opts.o sam_opts.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o sam_opts.o sam_opts.c
2018/01/30 19:11:46 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o cut_target.o cut_target.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o cut_target.o cut_target.c
2018/01/30 19:11:46 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o phase.o phase.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o phase.o phase.c
2018/01/30 19:11:47 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam2depth.o bam2depth.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bam2depth.o bam2depth.c
2018/01/30 19:11:47 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o padding.o padding.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o padding.o padding.c
2018/01/30 19:11:47 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bedcov.o bedcov.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bedcov.o bedcov.c
2018/01/30 19:11:47 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bamshuf.o bamshuf.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o bamshuf.o bamshuf.c
2018/01/30 19:11:48 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o faidx.o faidx.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o faidx.o faidx.c
2018/01/30 19:11:48 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o dict.o dict.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o dict.o dict.c
2018/01/30 19:11:48 ui: amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o stats.o stats.c
amazon-ebs: gcc -g -Wall -O2 -I. -Ihtslib-1.3.1 -c -o stats.o stats.c
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 Remote command exited without exit status or exit signal.
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 [INFO] RPC endpoint: Communicator ended with: 2300218
2018/01/30 19:12:34 [INFO] 1322906 bytes written for 'stdout'
2018/01/30 19:12:34 [INFO] 41887 bytes written for 'stderr'
2018/01/30 19:12:34 [INFO] RPC client: Communicator ended with: 2300218
2018/01/30 19:12:34 [INFO] RPC endpoint: Communicator ended with: 2300218
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 [INFO] 1322906 bytes written for 'stdout'
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 [INFO] 41887 bytes written for 'stderr'
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 [INFO] RPC client: Communicator ended with: 2300218
2018/01/30 19:12:34 [INFO] (telemetry) ending shell
2018/01/30 19:12:34 [INFO] (telemetry) found error: Script disconnected unexpectedly.
2018/01/30 19:12:34 ui: ==> amazon-ebs: Terminating the source AWS instance...
==> amazon-ebs: Terminating the source AWS instance...
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 Waiting for state to become: terminated
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 Using 2s as polling delay (change with AWS_POLL_DELAY_SECONDS)
2018/01/30 19:12:34 packer: 2018/01/30 19:12:34 Allowing 300s to complete (change with AWS_TIMEOUT_SECONDS)
2018/01/30 19:12:55 ui: ==> amazon-ebs: Cleaning up any extra volumes...
==> amazon-ebs: Cleaning up any extra volumes...
2018/01/30 19:12:55 ui: ==> amazon-ebs: No volumes to clean up, skipping
==> amazon-ebs: No volumes to clean up, skipping
2018/01/30 19:12:55 ui: ==> amazon-ebs: Deleting temporary security group...
==> amazon-ebs: Deleting temporary security group...
2018/01/30 19:12:55 ui: ==> amazon-ebs: Deleting temporary keypair...
==> amazon-ebs: Deleting temporary keypair...
2018/01/30 19:12:55 [INFO] (telemetry) ending amazon-ebs
2018/01/30 19:12:55 [INFO] (telemetry) found error: Script disconnected unexpectedly.
2018/01/30 19:12:55 ui error: Build 'amazon-ebs' errored: Script disconnected unexpectedly.
2018/01/30 19:12:55 Builds completed. Waiting on interrupt barrier...
2018/01/30 19:12:55 machine readable: error-count []string{"1"}
2018/01/30 19:12:55 ui error:
==> Some builds didn't complete successfully and had errors:
2018/01/30 19:12:55 machine readable: amazon-ebs,error []string{"Script disconnected unexpectedly."}
2018/01/30 19:12:55 ui error: --> amazon-ebs: Script disconnected unexpectedly.
2018/01/30 19:12:55 ui:
==> Builds finished but no artifacts were created.
Build 'amazon-ebs' errored: Script disconnected unexpectedly.
==> Some builds didn't complete successfully and had errors:
--> amazon-ebs: Script disconnected unexpectedly.
==> Builds finished but no artifacts were created.
2018/01/30 19:12:56 waiting for all plugin processes to complete...
2018/01/30 19:12:56 /usr/local/bin/packer: plugin process exited
2018/01/30 19:12:56 /usr/local/bin/packer: plugin process exited
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