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mcallaway/gist:e8c797bbae76162b47de

Created April 13, 2015 18:30
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build fails
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gistfile1.txt
```
... more ...
2015-04-13 13:26:10-0500 mcallawa-trusty: 2015/04/13 13:26:10 Genome::InstrumentData::AlignmentResult::Bwa id(TEST: >>tojaeyah5.10-929ec81<< bwa 0.5.9 [-t 4 -q 5::] on 6173R/4-TAGCTT (2851949190) for H_HY-03023 (2725316319) against NCBI-human-build36 (101947881) (88399148E20A11E49DE785073F0CD76F)): Oh no! Caught an exception while in the critical point where the BAM pipe was open: Failed to generate intermediate result!ERROR RUNNING COMMAND. Exit code 1 from: /opt/plenv/.plenv/versions/5.10.1/bin/perl5.10.1 -I /gscuser/mcallawa/git/genome/lib/perl/Genome/Site/TGI/SiteLib -e 'use above "Genome"; Genome::InstrumentData::IntermediateAlignmentResult->get_or_create(aligner_index_id => "f3df7303bda74e638982fedfc0774226", aligner_name => "bwa", aligner_params => "-t1 -q 5", aligner_version => "0.5.9", flagstat_file => "", input_file => "/tmp/211.tmpdir/gm-genome_sys-2015-04-13_13_26_02--k5f4/anonymous0/2851949190-sanger-fastq-0.fastq", input_pass => "1", instrument_data_id => "2851949190", instrument_data_segment_id => "", instrument_data_segment_type => "", samtools_version => "r963", test_name => "tojaeyah5.10-929ec81", trimmer_name => "", trimmer_params => "", trimmer_version => "", users => {"requestor" => Genome::Model::Build::ReferenceAlignment::Solexa->get(q{7BC31858E20A11E4985910073F0CD76F}), "sponsor" => Genome::Sys:
2015-04-13 13:26:10-0500 mcallawa-trusty: ERROR: Oh no! Caught an exception while in the critical point where the BAM pipe was open: Failed to generate intermediate result!ERROR RUNNING COMMAND. Exit code 1 from: /opt/plenv/.plenv/versions/5.10.1/bin/perl5.10.1 -I /gscuser/mcallawa/git/genome/lib/perl/Genome/Site/TGI/SiteLib -e 'use above "Genome"; Genome::InstrumentData::IntermediateAlignmentResult->get_or_create(aligner_index_id => "f3df7303bda74e638982fedfc0774226", aligner_name => "bwa", aligner_params => "-t1 -q 5", aligner_version => "0.5.9", flagstat_file => "", input_file => "/tmp/211.tmpdir/gm-genome_sys-2015-04-13_13_26_02--k5f4/anonymous0/2851949190-sanger-fastq-0.fastq", input_pass => "1", instrument_data_id => "2851949190", instrument_data_segment_id => "", instrument_data_segment_type => "", samtools_version => "r963", test_name => "tojaeyah5.10-929ec81", trimmer_name => "", trimmer_params => "", trimmer_version => "", users => {"requestor" => Genome::Model::Build::ReferenceAlignment::Solexa->get(q{7BC31858E20A11E4985910073F0CD76F}), "sponsor" => Genome::Sys::User->get(q{[email protected]}), }); UR::Context->commit;'
2015-04-13 13:26:10-0500 mcallawa-trusty: See the command's captured STDERR (if it exists) for more information at /gscuser/mcallawa/git/genome/lib/perl/Genome/InstrumentData/AlignmentResult/WithIntermediateResults.pm line 57.
2015-04-13 13:26:10-0500 mcallawa-trusty: [samopen] SAM header is present: 113 sequences.
2015-04-13 13:26:10-0500 mcallawa-trusty: [sam_read1] reference 'ID:2851949190 VN:0.5.9 CL:bwa aln -t1 -q 5; bwa sampe
2015-04-13 13:26:10-0500 mcallawa-trusty: 3-lib1 DS:paired end DT:2010-02-20 SM:H_HY-03023 CN:WUGSC
2015-04-13 13:26:10-0500 mcallawa-trusty: n-build36 M5:89bc15e39a1afe2c310afeaaec05306a SP:unknown
2015-04-13 13:26:10-0500 mcallawa-trusty: ' is recognized as '*'.
2015-04-13 13:26:10-0500 mcallawa-trusty: [main_samview] truncated file.
... more ...
```
@mcallaway
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mcallawa@mcallawa-trusty:~/git/genome$ ./bin/genome-env /opt/plenv/.plenv/versions/5.10.1/bin/perl5.10.1 -I /gscuser/mcallawa/git/genome/lib/perl/Genome/Site/TGI/SiteLib -e 'use above "Genome"; Genome::InstrumentData::IntermediateAlignmentResult->get_or_create(aligner_index_id => "f3df7303bda74e638982fedfc0774226", aligner_name => "bwa", aligner_params => "-t1 -q 5", aligner_version => "0.5.9", flagstat_file => "", input_file => "/tmp/211.tmpdir/gm-genome_sys-2015-04-13_13_26_02--k5f4/anonymous0/2851949190-sanger-fastq-0.fastq", input_pass => "1", instrument_data_id => "2851949190", instrument_data_segment_id => "", instrument_data_segment_type => "", samtools_version => "r963", test_name => "tojaeyah5.10-929ec81", trimmer_name => "", trimmer_params => "", trimmer_version => "", users => {"requestor" => Genome::Model::Build::ReferenceAlignment::Solexa->get(q{7BC31858E20A11E4985910073F0CD76F}), "sponsor" => Genome::Sys::User->get(q{[email protected]}), }); UR::Context->commit;' 2>&1 | tee ~/log2

=> Preparing Submodules...
   sqitch/genome: OK
   ur: OK
   workflow: OK

=> Rebuilding Meta DB............. done
=> Creating test database...
=> Migrating test database...warning: The core.pg config has been deprecated in favor of engine.pg.
warning: Run '/gscuser/mcallawa/carton_test/local/bin/sqitch engine update-config' to update your configurations.
 nothing to deploy

=> Setting Up Test Environment...

Genome Perl: 5.10.1
Genome Prove: TAP::Harness v3.35 and Perl v5.18.2
UR: /gscuser/mcallawa/git/genome/ur/lib/UR.pm
Workflow: /gscuser/mcallawa/git/genome/workflow/lib/Workflow.pm
Genome: /gscuser/mcallawa/git/genome/lib/perl/Genome.pm
Test DB Snapshot: 46a7998
Test DB Name: 0F6A103CE20D11E4A66AA8FEA9DCD391
Test DB Host: apipe-test-db.gsc.wustl.edu
Test DB Port: 5432

/opt/plenv/.plenv/versions/5.10.1/bin/perl5.10.1 -I /gscuser/mcallawa/git/genome/lib/perl/Genome/Site/TGI/SiteLib -e use above "Genome"; Genome::InstrumentData::IntermediateAlignmentResult->get_or_create(aligner_index_id => "f3df7303bda74e638982fedfc0774226", aligner_name => "bwa", aligner_params => "-t1 -q 5", aligner_version => "0.5.9", flagstat_file => "", input_file => "/tmp/211.tmpdir/gm-genome_sys-2015-04-13_13_26_02--k5f4/anonymous0/2851949190-sanger-fastq-0.fastq", input_pass => "1", instrument_data_id => "2851949190", instrument_data_segment_id => "", instrument_data_segment_type => "", samtools_version => "r963", test_name => "tojaeyah5.10-929ec81", trimmer_name => "", trimmer_params => "", trimmer_version => "", users => {"requestor" => Genome::Model::Build::ReferenceAlignment::Solexa->get(q{7BC31858E20A11E4985910073F0CD76F}), "sponsor" => Genome::Sys::User->get(q{[email protected]}), }); UR::Context->commit;...
The 'users' parameter ("HASH(0x5a16e08)") to Genome::SoftwareResult::User::with_registered_users did not pass the 'must contain sponsor and requestor' callback:
 at /gscuser/mcallawa/git/genome/lib/perl/Genome/SoftwareResult/User.pm line 50.
        Genome::SoftwareResult::User::with_registered_users(undef, "aligner_index_id", "f3df7303bda74e638982fedfc0774226", "aligner_name", "bwa", "aligner_params", "-t1 -q 5", "aligner_version", "0.5.9", ...) called at /gscuser/mcallawa/git/genome/lib/perl/Genome/SoftwareResult.pm line 262
        Genome::SoftwareResult::get_or_create("Genome::InstrumentData::IntermediateAlignmentResult", "aligner_index_id", "f3df7303bda74e638982fedfc0774226", "aligner_name", "bwa", "aligner_params", "-t1 -q 5", "aligner_version", "0.5.9", ...) called at -e line 1

@mcallaway
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2015-04-13 13:59:41-0500 mcallawa-trusty: DEBUG: OS is x86_64
2015-04-13 13:59:41-0500 mcallawa-trusty: DEBUG: Required OS is x86_64
2015-04-13 13:59:41-0500 mcallawa-trusty: DEBUG: Estimated disk for this data set: 30000000 kb
2015-04-13 13:59:41-0500 mcallawa-trusty: DEBUG: Check for available disk...
2015-04-13 13:59:43-0500 mcallawa-trusty: DEBUG: Found 136 disk volumes
2015-04-13 13:59:50-0500 mcallawa-trusty: DEBUG: Available disk: 515758368427 kb
2015-04-13 13:59:50-0500 mcallawa-trusty: DEBUG: Prepare working directories...
2015-04-13 13:59:50-0500 mcallawa-trusty: DEBUG: Staging path is /tmp/212.tmpdir/gm-genome_sys-2015-04-13_13_59_50--gC_0/alignment-mcallawa-trusty.gsc.wustl.edu-mcallawa-31569-3D71F646E20F11E4B550D
5283F0CD76F
2015-04-13 13:59:50-0500 mcallawa-trusty: DEBUG: Working path is /tmp/212.tmpdir/gm-genome_sys-2015-04-13_13_59_50--gC_0/anonymous0
2015-04-13 13:59:50-0500 mcallawa-trusty: DEBUG: Preparing the output directory...
2015-04-13 13:59:50-0500 mcallawa-trusty: DEBUG: Staging disk usage is 4 KB
2015-04-13 13:59:50-0500 mcallawa-trusty: Could not perform allocation action! at /gscuser/mcallawa/git/genome/lib/perl/Genome/Disk/Allocation.pm line 582.
2015-04-13 13:59:50-0500 mcallawa-trusty:       Genome::Disk::Allocation::_execute_system_command("Genome::Disk::Allocation", "_create", "owner_class_name", "Genome::InstrumentData::IntermediateAli
gnmentResult::Bwa", "kilobytes_requested", 4, "id", "431BFA10E20F11E4B550D5283F0CD76F", "allocation_path", ...) called at /gscuser/mcallawa/git/genome/lib/perl/Genome/Disk/Allocation.pm line 230
2015-04-13 13:59:50-0500 mcallawa-trusty:       Genome::Disk::Allocation::__ANON__() called at /gscuser/mcallawa/git/genome/lib/perl/Genome/Utility/Instrumentation.pm line 72
2015-04-13 13:59:50-0500 mcallawa-trusty:       eval {...} called at /gscuser/mcallawa/git/genome/lib/perl/Genome/Utility/Instrumentation.pm line 71
2015-04-13 13:59:50-0500 mcallawa-trusty:       Genome::Utility::Instrumentation::timer("disk.allocation.create") called at /gscuser/mcallawa/git/genome/lib/perl/Genome/Disk/Allocation.pm line 231
2015-04-13 13:59:50-0500 mcallawa-trusty:       Genome::Disk::Allocation::create("Genome::Disk::Allocation", "owner_class_name", "Genome::InstrumentData::IntermediateAlignmentResult::Bwa", "kilobyt
es_requested", 4, "owner_id", "3D71F646E20F11E4B550D5283F0CD76F", "allocation_path", "alignment_data/2851949190/alignment-mcallawa-trusty.gsc.wustl"..., ...) called at /gscuser/mcallawa/git/genome/
lib/perl/Genome/Disk/Allocation.pm line 206
2015-04-13 13:59:50-0500 mcallawa-trusty:       Genome::Disk::Allocation::allocate("Genome::Disk::Allocation", "owner_class_name", "Genome::InstrumentData::IntermediateAlignmentResult::Bwa", "kilob
ytes_requested", 4, "owner_id", "3D71F646E20F11E4B550D5283F0CD76F", "allocation_path", "alignment_data/2851949190/alignment-mcallawa-trusty.gsc.wustl"..., ...) called at /gscuser/mcallawa/git/genom
e/lib/perl/Genome/SoftwareResult.pm line 623

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