Created
June 29, 2015 13:04
-
-
Save mpschr/3799977323769ee2c1b5 to your computer and use it in GitHub Desktop.
Processing failed on GEMINI chunk load
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [2015-06-26T08:57Z] Timing: organize samples | |
| [2015-06-26T08:57Z] multiprocessing: organize_samples | |
| [2015-06-26T08:57Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T08:57Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T08:57Z] Testing minimum versions of installed programs | |
| [2015-06-26T08:57Z] Timing: alignment preparation | |
| [2015-06-26T08:57Z] multiprocessing: prep_align_inputs | |
| [2015-06-26T09:55Z] multiprocessing: disambiguate_split | |
| [2015-06-26T09:55Z] Timing: alignment | |
| [2015-06-26T09:55Z] multiprocessing: process_alignment | |
| [2015-06-26T09:55Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T09:55Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:00Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:00Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:04Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:04Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:09Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:09Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:13Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:14Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:17Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:18Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:21Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:22Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:25Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:25Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:28Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:29Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:32Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:33Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:36Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:36Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:40Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:44Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:47Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:48Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:50Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:54Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:55Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T10:57Z] multiprocessing: delayed_bam_merge | |
| [2015-06-26T11:26Z] Timing: callable regions | |
| [2015-06-26T11:26Z] multiprocessing: prep_samples | |
| [2015-06-26T11:26Z] multiprocessing: postprocess_alignment | |
| [2015-06-26T11:26Z] multiprocessing: calc_callable_loci | |
| [2015-06-26T11:26Z] multiprocessing: calc_callable_loci | |
| [2015-06-26T12:08Z] multiprocessing: combine_bed | |
| [2015-06-26T12:14Z] multiprocessing: combine_bed | |
| [2015-06-26T12:31Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T12:32Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-26T12:39Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T12:40Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-26T13:38Z] multiprocessing: combine_sample_regions | |
| [2015-06-26T13:39Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018051.0 | |
| 75%: 31018287.0 | |
| 95%: 31019038.35 | |
| 99%: 39112401.24 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 115.0 | |
| median: 161.0 | |
| 75%: 230.5 | |
| 95%: 709.7 | |
| 99%: 975.08 | |
| max: 1467 | |
| [2015-06-26T13:39Z] Timing: coverage | |
| [2015-06-26T13:39Z] Timing: structural variation initial | |
| [2015-06-26T13:39Z] Timing: alignment post-processing | |
| [2015-06-26T13:39Z] multiprocessing: piped_bamprep | |
| [2015-06-26T14:32Z] Timing: variant calling | |
| [2015-06-26T14:32Z] multiprocessing: variantcall_sample | |
| [2015-06-26T14:39Z] run local -- checkpoint passed: multicore | |
| [2015-06-26T14:39Z] Timing: organize samples | |
| [2015-06-26T14:39Z] multiprocessing: organize_samples | |
| [2015-06-26T14:39Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T14:39Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T14:39Z] Testing minimum versions of installed programs | |
| [2015-06-26T14:39Z] Timing: alignment preparation | |
| [2015-06-26T14:39Z] multiprocessing: prep_align_inputs | |
| [2015-06-26T14:39Z] multiprocessing: disambiguate_split | |
| [2015-06-26T14:39Z] Timing: alignment | |
| [2015-06-26T14:39Z] multiprocessing: process_alignment | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:39Z] multiprocessing: delayed_bam_merge | |
| [2015-06-26T14:39Z] Timing: callable regions | |
| [2015-06-26T14:39Z] multiprocessing: prep_samples | |
| [2015-06-26T14:39Z] multiprocessing: postprocess_alignment | |
| [2015-06-26T14:39Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T14:39Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-26T14:40Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T14:40Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-26T14:40Z] multiprocessing: combine_sample_regions | |
| [2015-06-26T14:40Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018051.0 | |
| 75%: 31018287.0 | |
| 95%: 31019038.35 | |
| 99%: 39112401.24 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 115.0 | |
| median: 161.0 | |
| 75%: 230.5 | |
| 95%: 709.7 | |
| 99%: 975.08 | |
| max: 1467 | |
| [2015-06-26T14:40Z] Timing: coverage | |
| [2015-06-26T14:40Z] Timing: structural variation initial | |
| [2015-06-26T14:40Z] Timing: alignment post-processing | |
| [2015-06-26T14:40Z] multiprocessing: piped_bamprep | |
| [2015-06-26T14:40Z] Timing: variant calling | |
| [2015-06-26T14:40Z] multiprocessing: variantcall_sample | |
| [2015-06-26T14:43Z] run local -- checkpoint passed: multicore | |
| [2015-06-26T14:43Z] Timing: organize samples | |
| [2015-06-26T14:43Z] multiprocessing: organize_samples | |
| [2015-06-26T14:43Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T14:43Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T14:43Z] Testing minimum versions of installed programs | |
| [2015-06-26T14:43Z] Timing: alignment preparation | |
| [2015-06-26T14:43Z] multiprocessing: prep_align_inputs | |
| [2015-06-26T14:43Z] multiprocessing: disambiguate_split | |
| [2015-06-26T14:43Z] Timing: alignment | |
| [2015-06-26T14:43Z] multiprocessing: process_alignment | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T14:43Z] multiprocessing: delayed_bam_merge | |
| [2015-06-26T14:43Z] Timing: callable regions | |
| [2015-06-26T14:43Z] multiprocessing: prep_samples | |
| [2015-06-26T14:43Z] multiprocessing: postprocess_alignment | |
| [2015-06-26T14:43Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T14:43Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-26T14:43Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T14:43Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-26T14:43Z] multiprocessing: combine_sample_regions | |
| [2015-06-26T14:43Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018051.0 | |
| 75%: 31018287.0 | |
| 95%: 31019038.35 | |
| 99%: 39112401.24 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 115.0 | |
| median: 161.0 | |
| 75%: 230.5 | |
| 95%: 709.7 | |
| 99%: 975.08 | |
| max: 1467 | |
| [2015-06-26T14:43Z] Timing: coverage | |
| [2015-06-26T14:43Z] Timing: structural variation initial | |
| [2015-06-26T14:43Z] Timing: alignment post-processing | |
| [2015-06-26T14:43Z] multiprocessing: piped_bamprep | |
| [2015-06-26T14:43Z] Timing: variant calling | |
| [2015-06-26T14:43Z] multiprocessing: variantcall_sample | |
| [2015-06-26T15:08Z] run local -- checkpoint passed: multicore | |
| [2015-06-26T15:08Z] Timing: organize samples | |
| [2015-06-26T15:08Z] multiprocessing: organize_samples | |
| [2015-06-26T15:08Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T15:08Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T15:08Z] Testing minimum versions of installed programs | |
| [2015-06-26T15:08Z] Timing: alignment preparation | |
| [2015-06-26T15:08Z] multiprocessing: prep_align_inputs | |
| [2015-06-26T15:08Z] multiprocessing: disambiguate_split | |
| [2015-06-26T15:08Z] Timing: alignment | |
| [2015-06-26T15:08Z] multiprocessing: process_alignment | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T15:08Z] multiprocessing: delayed_bam_merge | |
| [2015-06-26T15:08Z] Timing: callable regions | |
| [2015-06-26T15:08Z] multiprocessing: prep_samples | |
| [2015-06-26T15:08Z] multiprocessing: postprocess_alignment | |
| [2015-06-26T15:08Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T15:08Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-26T15:08Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T15:08Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-26T15:08Z] multiprocessing: combine_sample_regions | |
| [2015-06-26T15:10Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018054.0 | |
| 75%: 31018315.75 | |
| 95%: 31019674.2 | |
| 99%: 39112482.15 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 119.0 | |
| median: 162.0 | |
| 75%: 247.5 | |
| 95%: 709.7 | |
| 99%: 1180.16 | |
| max: 2078 | |
| [2015-06-26T15:10Z] Timing: coverage | |
| [2015-06-26T15:10Z] Timing: structural variation initial | |
| [2015-06-26T15:10Z] Timing: alignment post-processing | |
| [2015-06-26T15:10Z] multiprocessing: piped_bamprep | |
| [2015-06-26T15:41Z] Timing: variant calling | |
| [2015-06-26T15:41Z] multiprocessing: variantcall_sample | |
| [2015-06-26T15:44Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:235595206-249250621 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpuFbrGa/batch01-1_235595205_249250621-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpuFbrGa/tx/tmpmLKH1a/batch01-1_235595205_249250621-raw.vcf.gz | |
| Error at 1:235596681: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:126345722-157364296 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp2BtlEl/batch01-2_126345721_157364296-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp2BtlEl/tx/tmpvDmBpq/batch01-2_126345721_157364296-raw.vcf.gz | |
| Error at 2:126347753: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:62037259-93055319 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpFdMTPl/batch01-1_62037258_93055319-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpFdMTPl/tx/tmpKIW2Lo/batch01-1_62037258_93055319-raw.vcf.gz | |
| Error at 1:62039007: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:93056190-142539830 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpuGN1CW/batch01-1_93056189_142539830-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpuGN1CW/tx/tmpYxzKKD/batch01-1_93056189_142539830-raw.vcf.gz | |
| Error at 1:93057541: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:1-31018999 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpQWK1Tl/batch01-3_0_31018999-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpQWK1Tl/tx/tmpvqjepq/batch01-3_0_31018999-raw.vcf.gz | |
| Error at 3:74748: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:157364413-188382830 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpQQMNLf/batch01-2_157364412_188382830-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpQQMNLf/tx/tmp0t6C0E/batch01-2_157364412_188382830-raw.vcf.gz | |
| Error at 2:157371857: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:31018824-62036934 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpaY926M/batch01-2_31018823_62036934-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpaY926M/tx/tmpu8idKZ/batch01-2_31018823_62036934-raw.vcf.gz | |
| Error at 2:31022818: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:62037134-95326413 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpqyLqXE/batch01-2_62037133_95326413-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpqyLqXE/tx/tmp7TgY2D/batch01-2_62037133_95326413-raw.vcf.gz | |
| Error at 2:62043728: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:173558319-204576375 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpHq4Loy/batch01-1_173558318_204576375-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpHq4Loy/tx/tmpbPHG2J/batch01-1_173558318_204576375-raw.vcf.gz | |
| Error at 1:173562419: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:188382932-219401300 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpxGA8W2/batch01-2_188382931_219401300-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpxGA8W2/tx/tmpsmWEl4/batch01-2_188382931_219401300-raw.vcf.gz | |
| Error at 2:188387618: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:47Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:219401516-243199373 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpk7m8Ak/batch01-2_219401515_243199373-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpk7m8Ak/tx/tmpKxSf3Q/batch01-2_219401515_243199373-raw.vcf.gz | |
| Error at 2:219403827: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:48Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:95326515-126345569 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp8hI5cH/batch01-2_95326514_126345569-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp8hI5cH/tx/tmpaz8kkR/batch01-2_95326514_126345569-raw.vcf.gz | |
| Error at 2:95346064: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:48Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:204576477-235594648 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpSar9OC/batch01-1_204576476_235594648-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpSar9OC/tx/tmpwQ_TjB/batch01-1_204576476_235594648-raw.vcf.gz | |
| Error at 1:204583450: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:48Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:1-31018107 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpkybK0N/batch01-2_0_31018107-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpkybK0N/tx/tmphCPipI/batch01-2_0_31018107-raw.vcf.gz | |
| Error at 2:13074: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:49Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 4:186110713-191154276 `cat /home/michael/Documents/projects/exon/scratch/vardict/4/tx/tmp8x3PPN/batch01-4_186110712_191154276-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/4/tx/tmp8x3PPN/tx/tmp1BUtUF/batch01-4_186110712_191154276-raw.vcf.gz | |
| Error at 4:186111639: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:50Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:186562086-198022430 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpBlT96k/batch01-3_186562085_198022430-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpBlT96k/tx/tmpKcFM4p/batch01-3_186562085_198022430-raw.vcf.gz | |
| Error at 3:186562284: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:50Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:31018917-62037157 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpktXQx9/batch01-1_31018916_62037157-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpktXQx9/tx/tmpanKnui/batch01-1_31018916_62037157-raw.vcf.gz | |
| Error at 1:31022237: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:50Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:142539965-173558159 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpImZRUd/batch01-1_142539964_173558159-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpImZRUd/tx/tmpif6bqj/batch01-1_142539964_173558159-raw.vcf.gz | |
| Error at 1:142539993: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:51Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:62037444-93505141 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpCwPKQr/batch01-3_62037443_93505141-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpCwPKQr/tx/tmp6BdByZ/batch01-3_62037443_93505141-raw.vcf.gz | |
| Error at 3:62045678: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T15:52Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:1-31018657 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpDTK5Z8/batch01-1_0_31018657-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpDTK5Z8/tx/tmpHUOeYp/batch01-1_0_31018657-raw.vcf.gz | |
| Error at 1:10109: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:26Z] run local -- checkpoint passed: multicore | |
| [2015-06-26T23:26Z] Timing: organize samples | |
| [2015-06-26T23:26Z] multiprocessing: organize_samples | |
| [2015-06-26T23:26Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T23:26Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-26T23:26Z] Testing minimum versions of installed programs | |
| [2015-06-26T23:26Z] Timing: alignment preparation | |
| [2015-06-26T23:26Z] multiprocessing: prep_align_inputs | |
| [2015-06-26T23:26Z] multiprocessing: disambiguate_split | |
| [2015-06-26T23:26Z] Timing: alignment | |
| [2015-06-26T23:26Z] multiprocessing: process_alignment | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-26T23:26Z] multiprocessing: delayed_bam_merge | |
| [2015-06-26T23:26Z] Timing: callable regions | |
| [2015-06-26T23:26Z] multiprocessing: prep_samples | |
| [2015-06-26T23:26Z] multiprocessing: postprocess_alignment | |
| [2015-06-26T23:26Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T23:26Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-26T23:26Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-26T23:26Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-26T23:26Z] multiprocessing: combine_sample_regions | |
| [2015-06-26T23:26Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018054.0 | |
| 75%: 31018315.75 | |
| 95%: 31019674.2 | |
| 99%: 39112482.15 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 119.0 | |
| median: 162.0 | |
| 75%: 247.5 | |
| 95%: 709.7 | |
| 99%: 1180.16 | |
| max: 2078 | |
| [2015-06-26T23:26Z] Timing: coverage | |
| [2015-06-26T23:26Z] Timing: structural variation initial | |
| [2015-06-26T23:26Z] Timing: alignment post-processing | |
| [2015-06-26T23:26Z] multiprocessing: piped_bamprep | |
| [2015-06-26T23:26Z] Timing: variant calling | |
| [2015-06-26T23:26Z] multiprocessing: variantcall_sample | |
| [2015-06-26T23:29Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:235595206-249250621 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpOw49nT/batch01-1_235595205_249250621-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpOw49nT/tx/tmpIbVwfA/batch01-1_235595205_249250621-raw.vcf.gz | |
| Error at 1:235596681: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:32Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:126345722-157364296 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpbvygUX/batch01-2_126345721_157364296-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpbvygUX/tx/tmpqSynAk/batch01-2_126345721_157364296-raw.vcf.gz | |
| Error at 2:126347753: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:32Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:62037259-93055319 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpXAoNrM/batch01-1_62037258_93055319-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpXAoNrM/tx/tmp0sioLH/batch01-1_62037258_93055319-raw.vcf.gz | |
| Error at 1:62039007: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:32Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:1-31018999 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpDGyLlf/batch01-3_0_31018999-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpDGyLlf/tx/tmpeehE0o/batch01-3_0_31018999-raw.vcf.gz | |
| Error at 3:74748: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:32Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:93056190-142539830 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpf08tq2/batch01-1_93056189_142539830-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpf08tq2/tx/tmpzLHePr/batch01-1_93056189_142539830-raw.vcf.gz | |
| Error at 1:93057541: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:32Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:157364413-188382830 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpJa60Hr/batch01-2_157364412_188382830-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpJa60Hr/tx/tmpC3OQzA/batch01-2_157364412_188382830-raw.vcf.gz | |
| Error at 2:157371857: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:31018824-62036934 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp0Tpo8c/batch01-2_31018823_62036934-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp0Tpo8c/tx/tmpmvoFUG/batch01-2_31018823_62036934-raw.vcf.gz | |
| Error at 2:31022818: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:62037134-95326413 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp74SdYC/batch01-2_62037133_95326413-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp74SdYC/tx/tmpjAIdlY/batch01-2_62037133_95326413-raw.vcf.gz | |
| Error at 2:62043728: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:188382932-219401300 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpl1n577/batch01-2_188382931_219401300-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpl1n577/tx/tmpKEQLfa/batch01-2_188382931_219401300-raw.vcf.gz | |
| Error at 2:188387618: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:219401516-243199373 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpaHvCna/batch01-2_219401515_243199373-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpaHvCna/tx/tmpASz8l8/batch01-2_219401515_243199373-raw.vcf.gz | |
| Error at 2:219403827: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:95326515-126345569 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpGvEkL2/batch01-2_95326514_126345569-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpGvEkL2/tx/tmp9vPd6j/batch01-2_95326514_126345569-raw.vcf.gz | |
| Error at 2:95346064: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:173558319-204576375 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpLX65Pq/batch01-1_173558318_204576375-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpLX65Pq/tx/tmpfcfKWo/batch01-1_173558318_204576375-raw.vcf.gz | |
| Error at 1:173562419: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:204576477-235594648 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpaBjLHH/batch01-1_204576476_235594648-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpaBjLHH/tx/tmp5PjNFJ/batch01-1_204576476_235594648-raw.vcf.gz | |
| Error at 1:204583450: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:33Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:1-31018107 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpsKiWXk/batch01-2_0_31018107-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpsKiWXk/tx/tmpFJ9WVl/batch01-2_0_31018107-raw.vcf.gz | |
| Error at 2:13074: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:35Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 4:186110713-191154276 `cat /home/michael/Documents/projects/exon/scratch/vardict/4/tx/tmpykVdqe/batch01-4_186110712_191154276-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/4/tx/tmpykVdqe/tx/tmpkzcaeQ/batch01-4_186110712_191154276-raw.vcf.gz | |
| Error at 4:186111639: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:35Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:186562086-198022430 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpw0WY55/batch01-3_186562085_198022430-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpw0WY55/tx/tmpTpScxV/batch01-3_186562085_198022430-raw.vcf.gz | |
| Error at 3:186562284: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:35Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:31018917-62037157 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmp0CoIuI/batch01-1_31018916_62037157-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmp0CoIuI/tx/tmppbTZYt/batch01-1_31018916_62037157-raw.vcf.gz | |
| Error at 1:31022237: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:36Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:142539965-173558159 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpG81k0p/batch01-1_142539964_173558159-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpG81k0p/tx/tmpHX0buS/batch01-1_142539964_173558159-raw.vcf.gz | |
| Error at 1:142539993: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:36Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:62037444-93505141 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpnZ1_kE/batch01-3_62037443_93505141-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpnZ1_kE/tx/tmpm6g8y0/batch01-3_62037443_93505141-raw.vcf.gz | |
| Error at 3:62045678: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-26T23:37Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:1-31018657 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpLJIXZO/batch01-1_0_31018657-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpLJIXZO/tx/tmpJGQ_ws/batch01-1_0_31018657-raw.vcf.gz | |
| Error at 1:10109: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:11Z] run local -- checkpoint passed: multicore | |
| [2015-06-29T07:11Z] Timing: organize samples | |
| [2015-06-29T07:11Z] multiprocessing: organize_samples | |
| [2015-06-29T07:11Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-29T07:11Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-29T07:11Z] Testing minimum versions of installed programs | |
| [2015-06-29T07:11Z] Timing: alignment preparation | |
| [2015-06-29T07:11Z] multiprocessing: prep_align_inputs | |
| [2015-06-29T07:11Z] multiprocessing: disambiguate_split | |
| [2015-06-29T07:11Z] Timing: alignment | |
| [2015-06-29T07:11Z] multiprocessing: process_alignment | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:11Z] multiprocessing: delayed_bam_merge | |
| [2015-06-29T07:11Z] Timing: callable regions | |
| [2015-06-29T07:11Z] multiprocessing: prep_samples | |
| [2015-06-29T07:11Z] multiprocessing: postprocess_alignment | |
| [2015-06-29T07:12Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-29T07:12Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-29T07:12Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-29T07:12Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-29T07:12Z] multiprocessing: combine_sample_regions | |
| [2015-06-29T07:12Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018054.0 | |
| 75%: 31018315.75 | |
| 95%: 31019674.2 | |
| 99%: 39112482.15 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 119.0 | |
| median: 162.0 | |
| 75%: 247.5 | |
| 95%: 709.7 | |
| 99%: 1180.16 | |
| max: 2078 | |
| [2015-06-29T07:12Z] Timing: coverage | |
| [2015-06-29T07:12Z] Timing: structural variation initial | |
| [2015-06-29T07:12Z] Timing: alignment post-processing | |
| [2015-06-29T07:12Z] multiprocessing: piped_bamprep | |
| [2015-06-29T07:12Z] Timing: variant calling | |
| [2015-06-29T07:12Z] multiprocessing: variantcall_sample | |
| [2015-06-29T07:15Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:235595206-249250621 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpCT4Lb8/batch01-1_235595205_249250621-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpCT4Lb8/tx/tmp4V2xHS/batch01-1_235595205_249250621-raw.vcf.gz | |
| Error at 1:235596681: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:126345722-157364296 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpa4bt5x/batch01-2_126345721_157364296-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpa4bt5x/tx/tmpHGiwBr/batch01-2_126345721_157364296-raw.vcf.gz | |
| Error at 2:126347753: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:62037259-93055319 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpnLad6P/batch01-1_62037258_93055319-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpnLad6P/tx/tmpkvBK_j/batch01-1_62037258_93055319-raw.vcf.gz | |
| Error at 1:62039007: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:1-31018999 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpcspSh7/batch01-3_0_31018999-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpcspSh7/tx/tmpdRG3er/batch01-3_0_31018999-raw.vcf.gz | |
| Error at 3:74748: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:93056190-142539830 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpq_Kjz8/batch01-1_93056189_142539830-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpq_Kjz8/tx/tmpFuU_NY/batch01-1_93056189_142539830-raw.vcf.gz | |
| Error at 1:93057541: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:157364413-188382830 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpWCEd3q/batch01-2_157364412_188382830-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpWCEd3q/tx/tmpDmFTpe/batch01-2_157364412_188382830-raw.vcf.gz | |
| Error at 2:157371857: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:188382932-219401300 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp4Xw7ZP/batch01-2_188382931_219401300-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp4Xw7ZP/tx/tmpT51W7B/batch01-2_188382931_219401300-raw.vcf.gz | |
| Error at 2:188387618: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:62037134-95326413 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpWKQb5e/batch01-2_62037133_95326413-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpWKQb5e/tx/tmpB0YdNL/batch01-2_62037133_95326413-raw.vcf.gz | |
| Error at 2:62043728: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:18Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:31018824-62036934 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpmJBhLf/batch01-2_31018823_62036934-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpmJBhLf/tx/tmpaGXn1X/batch01-2_31018823_62036934-raw.vcf.gz | |
| Error at 2:31022818: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:19Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:173558319-204576375 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpA8485R/batch01-1_173558318_204576375-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpA8485R/tx/tmpBz_otp/batch01-1_173558318_204576375-raw.vcf.gz | |
| Error at 1:173562419: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:19Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:95326515-126345569 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpfpuklW/batch01-2_95326514_126345569-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpfpuklW/tx/tmpf2zY0x/batch01-2_95326514_126345569-raw.vcf.gz | |
| Error at 2:95346064: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:19Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:219401516-243199373 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp4kX9qc/batch01-2_219401515_243199373-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmp4kX9qc/tx/tmpLoOtZ_/batch01-2_219401515_243199373-raw.vcf.gz | |
| Error at 2:219403827: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:19Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 2:1-31018107 `cat /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpubmWki/batch01-2_0_31018107-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/2/tx/tmpubmWki/tx/tmpu78xfM/batch01-2_0_31018107-raw.vcf.gz | |
| Error at 2:13074: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:19Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:204576477-235594648 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpuJv9iZ/batch01-1_204576476_235594648-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpuJv9iZ/tx/tmpISP0Dr/batch01-1_204576476_235594648-raw.vcf.gz | |
| Error at 1:204583450: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:20Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 4:186110713-191154276 `cat /home/michael/Documents/projects/exon/scratch/vardict/4/tx/tmpDZMpt7/batch01-4_186110712_191154276-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/4/tx/tmpDZMpt7/tx/tmpDH6ENO/batch01-4_186110712_191154276-raw.vcf.gz | |
| Error at 4:186111639: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:21Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:31018917-62037157 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmp2U6Vm7/batch01-1_31018916_62037157-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmp2U6Vm7/tx/tmpSgAHfY/batch01-1_31018916_62037157-raw.vcf.gz | |
| Error at 1:31022237: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:21Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:186562086-198022430 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpnrdaty/batch01-3_186562085_198022430-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpnrdaty/tx/tmp2eS2bY/batch01-3_186562085_198022430-raw.vcf.gz | |
| Error at 3:186562284: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:21Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:142539965-173558159 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmptFbfrF/batch01-1_142539964_173558159-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmptFbfrF/tx/tmpj4n8kg/batch01-1_142539964_173558159-raw.vcf.gz | |
| Error at 1:142539993: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:22Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 3:62037444-93505141 `cat /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpWy4heE/batch01-3_62037443_93505141-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/3/tx/tmpWy4heE/tx/tmpEwJDFA/batch01-3_62037443_93505141-raw.vcf.gz | |
| Error at 3:62045678: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:23Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/bcftools merge -O z -r 1:1-31018657 `cat /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpVnK18J/batch01-1_0_31018657-raw-files.txt` > /home/michael/Documents/projects/exon/scratch/vardict/1/tx/tmpVnK18J/tx/tmpjzueIN/batch01-1_0_31018657-raw.vcf.gz | |
| Error at 1:10109: wrong number of fields in LSEQ? | |
| ' returned non-zero exit status 255 | |
| [2015-06-29T07:46Z] run local -- checkpoint passed: multicore | |
| [2015-06-29T07:46Z] Timing: organize samples | |
| [2015-06-29T07:46Z] multiprocessing: organize_samples | |
| [2015-06-29T07:46Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-29T07:46Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-29T07:46Z] Testing minimum versions of installed programs | |
| [2015-06-29T07:46Z] Timing: alignment preparation | |
| [2015-06-29T07:46Z] multiprocessing: prep_align_inputs | |
| [2015-06-29T07:46Z] multiprocessing: disambiguate_split | |
| [2015-06-29T07:46Z] Timing: alignment | |
| [2015-06-29T07:46Z] multiprocessing: process_alignment | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T07:46Z] multiprocessing: delayed_bam_merge | |
| [2015-06-29T07:46Z] Timing: callable regions | |
| [2015-06-29T07:46Z] multiprocessing: prep_samples | |
| [2015-06-29T07:46Z] multiprocessing: postprocess_alignment | |
| [2015-06-29T07:46Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-29T07:46Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-29T07:47Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-29T07:47Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-29T07:47Z] multiprocessing: combine_sample_regions | |
| [2015-06-29T07:48Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018051.0 | |
| 75%: 31018287.0 | |
| 95%: 31019038.35 | |
| 99%: 39112401.24 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 115.0 | |
| median: 161.0 | |
| 75%: 230.5 | |
| 95%: 709.7 | |
| 99%: 975.08 | |
| max: 1467 | |
| [2015-06-29T07:48Z] Timing: coverage | |
| [2015-06-29T07:48Z] Timing: structural variation initial | |
| [2015-06-29T07:48Z] Timing: alignment post-processing | |
| [2015-06-29T07:48Z] multiprocessing: piped_bamprep | |
| [2015-06-29T07:48Z] Timing: variant calling | |
| [2015-06-29T07:48Z] multiprocessing: variantcall_sample | |
| [2015-06-29T11:10Z] multiprocessing: concat_variant_files | |
| [2015-06-29T11:10Z] Timing: joint squaring off/backfilling | |
| [2015-06-29T11:10Z] Timing: variant post-processing | |
| [2015-06-29T11:10Z] multiprocessing: postprocess_variants | |
| [2015-06-29T11:10Z] Finalizing variant calls: Sample_PEZZ, vardict | |
| [2015-06-29T11:10Z] Calculating variation effects for Sample_PEZZ, vardict | |
| [2015-06-29T11:10Z] Finalizing variant calls: Sample_PEZZ, mutect | |
| [2015-06-29T11:10Z] Calculating variation effects for Sample_PEZZ, mutect | |
| [2015-06-29T11:12Z] Filtering for Sample_PEZZ, mutect | |
| [2015-06-29T11:12Z] Prioritization for Sample_PEZZ, mutect | |
| [2015-06-29T11:15Z] Filtering for Sample_PEZZ, vardict | |
| [2015-06-29T11:16Z] Prioritization for Sample_PEZZ, vardict | |
| [2015-06-29T11:31Z] Finalizing variant calls: Sample_PEZZ, freebayes | |
| [2015-06-29T11:31Z] Calculating variation effects for Sample_PEZZ, freebayes | |
| [2015-06-29T11:35Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/gemini load --passonly --skip-cadd --skip-gerp-bp -v /home/michael/Documents/projects/exon/scratch/vardict/batch02-effects-ploidyfix.vcf.gz -t snpEff --cores 10 --tempdir /home/michael/Documents/projects/exon/scratch/vardict/tx/tmpPG8Cal /home/michael/Documents/projects/exon/scratch/vardict/tx/tmpPG8Cal/batch02-effects-ploidyfix.db | |
| pid 25241: 85916 variants processed. | |
| pid 25241: 10075 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch02-effects-ploidyfix.vcf.chunk1.db.vcf' | |
| pid 25259: 79999 variants processed. | |
| pid 25262: 85603 variants processed. | |
| pid 25262: 10388 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch02-effects-ploidyfix.vcf.chunk8.db.vcf' | |
| pid 25253: 84561 variants processed. | |
| pid 25253: 11430 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch02-effects-ploidyfix.vcf.chunk5.db.vcf' | |
| pid 25256: 89104 variants processed. | |
| pid 25256: 6887 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch02-effects-ploidyfix.vcf.chunk6.db.vcf' | |
| pid 25259: 83939 variants processed. | |
| pid 25259: 12052 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch02-effects-ploidyfix.vcf.chunk7.db.vcf' | |
| Indexing /home/michael/Documents/projects/exon/scratch/vardict/batch02-effects-ploidyfix.vcf.gz with grabix. | |
| Loading 959912 variants. | |
| Breaking /home/michael/Documents/projects/exon/scratch/vardict/batch02-effects-ploidyfix.vcf.gz into 10 chunks. | |
| Loading chunk 0. | |
| Loading chunk 1. | |
| Loading chunk 2. | |
| Loading chunk 3. | |
| Loading chunk 4. | |
| Loading chunk 5. | |
| Loading chunk 6. | |
| Loading chunk 7. | |
| Loading chunk 8. | |
| Loading chunk 9. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 196, in load_fn | |
| gemini_load.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 50, in load | |
| load_multicore(args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 80, in load_multicore | |
| chunks = load_chunks_multicore(grabix_file, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 247, in load_chunks_multicore | |
| wait_until_finished(procs) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 338, in wait_until_finished | |
| raise ValueError("Processing failed on GEMINI chunk load") | |
| ValueError: Processing failed on GEMINI chunk load | |
| ' returned non-zero exit status 1 | |
| [2015-06-29T11:35Z] Finalizing variant calls: Sample_AEXX, vardict | |
| [2015-06-29T11:35Z] Calculating variation effects for Sample_AEXX, vardict | |
| [2015-06-29T11:51Z] run local -- checkpoint passed: multicore | |
| [2015-06-29T11:51Z] Timing: organize samples | |
| [2015-06-29T11:51Z] multiprocessing: organize_samples | |
| [2015-06-29T11:51Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-29T11:51Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml | |
| [2015-06-29T11:51Z] Testing minimum versions of installed programs | |
| [2015-06-29T11:51Z] Timing: alignment preparation | |
| [2015-06-29T11:51Z] multiprocessing: prep_align_inputs | |
| [2015-06-29T11:51Z] multiprocessing: disambiguate_split | |
| [2015-06-29T11:51Z] Timing: alignment | |
| [2015-06-29T11:51Z] multiprocessing: process_alignment | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 1_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] Aligning lane 2_2014.06.26_multisample with bwa aligner | |
| [2015-06-29T11:51Z] multiprocessing: delayed_bam_merge | |
| [2015-06-29T11:51Z] Timing: callable regions | |
| [2015-06-29T11:51Z] multiprocessing: prep_samples | |
| [2015-06-29T11:51Z] multiprocessing: postprocess_alignment | |
| [2015-06-29T11:51Z] Assigned coverage as 'amplicon' with 13.9% genome coverage and 0.0% offtarget coverage | |
| [2015-06-29T11:51Z] Recalibrating ['', 'Sample_PEZZ'] with GATK | |
| [2015-06-29T11:51Z] Assigned coverage as 'amplicon' with 12.5% genome coverage and 0.0% offtarget coverage | |
| [2015-06-29T11:51Z] Recalibrating ['', 'Sample_AEXX'] with GATK | |
| [2015-06-29T11:51Z] multiprocessing: combine_sample_regions | |
| [2015-06-29T11:51Z] Identified 170 parallel analysis blocks | |
| Block sizes: | |
| min: 1295 | |
| 5%: 27304.0 | |
| 25%: 164277.75 | |
| median: 31018051.0 | |
| 75%: 31018287.0 | |
| 95%: 31019038.35 | |
| 99%: 39112401.24 | |
| max: 58819520 | |
| Between block sizes: | |
| min: 101 | |
| 5%: 101.0 | |
| 25%: 115.0 | |
| median: 161.0 | |
| 75%: 230.5 | |
| 95%: 709.7 | |
| 99%: 975.08 | |
| max: 1467 | |
| [2015-06-29T11:51Z] Timing: coverage | |
| [2015-06-29T11:51Z] Timing: structural variation initial | |
| [2015-06-29T11:51Z] run local -- checkpoint passed: full | |
| [2015-06-29T11:51Z] Timing: alignment post-processing | |
| [2015-06-29T11:51Z] multiprocessing: piped_bamprep | |
| [2015-06-29T11:51Z] Timing: variant calling | |
| [2015-06-29T11:51Z] multiprocessing: variantcall_sample | |
| [2015-06-29T11:51Z] multiprocessing: concat_variant_files | |
| [2015-06-29T11:51Z] Timing: joint squaring off/backfilling | |
| [2015-06-29T11:51Z] Timing: variant post-processing | |
| [2015-06-29T11:51Z] multiprocessing: postprocess_variants | |
| [2015-06-29T11:51Z] Finalizing variant calls: Sample_PEZZ, vardict | |
| [2015-06-29T11:51Z] Calculating variation effects for Sample_PEZZ, vardict | |
| [2015-06-29T11:51Z] Filtering for Sample_PEZZ, vardict | |
| [2015-06-29T11:51Z] Prioritization for Sample_PEZZ, vardict | |
| [2015-06-29T11:51Z] Finalizing variant calls: Sample_PEZZ, mutect | |
| [2015-06-29T11:51Z] Calculating variation effects for Sample_PEZZ, mutect | |
| [2015-06-29T11:51Z] Filtering for Sample_PEZZ, mutect | |
| [2015-06-29T11:51Z] Prioritization for Sample_PEZZ, mutect | |
| [2015-06-29T11:54Z] Finalizing variant calls: Sample_PEZZ, freebayes | |
| [2015-06-29T11:54Z] Calculating variation effects for Sample_PEZZ, freebayes | |
| [2015-06-29T11:59Z] Filtering for Sample_PEZZ, freebayes | |
| [2015-06-29T12:00Z] Prioritization for Sample_PEZZ, freebayes | |
| [2015-06-29T12:21Z] Finalizing variant calls: Sample_AEXX, vardict | |
| [2015-06-29T12:21Z] Calculating variation effects for Sample_AEXX, vardict | |
| [2015-06-29T12:26Z] Filtering for Sample_AEXX, vardict | |
| [2015-06-29T12:26Z] Finalizing variant calls: Sample_AEXX, mutect | |
| [2015-06-29T12:26Z] Calculating variation effects for Sample_AEXX, mutect | |
| [2015-06-29T12:26Z] Prioritization for Sample_AEXX, vardict | |
| [2015-06-29T12:29Z] Filtering for Sample_AEXX, mutect | |
| [2015-06-29T12:29Z] Prioritization for Sample_AEXX, mutect | |
| [2015-06-29T12:46Z] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /home/michael/bin/bcbionextgen/tools/bin/gemini load --passonly --skip-cadd --skip-gerp-bp -v /home/michael/Documents/projects/exon/scratch/vardict/batch01-effects-ploidyfix.vcf.gz -t snpEff --cores 10 --tempdir /home/michael/Documents/projects/exon/scratch/vardict/tx/tmpghJoqz /home/michael/Documents/projects/exon/scratch/vardict/tx/tmpghJoqz/batch01-effects-ploidyfix.db | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch01-effects-ploidyfix.vcf.chunk3.db.vcf' | |
| pid 27724: 74951 variants processed. | |
| pid 27724: 11486 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch01-effects-ploidyfix.vcf.chunk5.db.vcf' | |
| pid 27727: 80449 variants processed. | |
| pid 27727: 5988 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch01-effects-ploidyfix.vcf.chunk6.db.vcf' | |
| pid 27709: 78499 variants processed. | |
| pid 27709: 7938 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch01-effects-ploidyfix.vcf.chunk0.db.vcf' | |
| pid 27712: 76864 variants processed. | |
| pid 27712: 9573 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch01-effects-ploidyfix.vcf.chunk1.db.vcf' | |
| pid 27721: 76766 variants processed. | |
| pid 27721: 9671 skipped due to having the FILTER field set. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 291, in loadchunk_fn | |
| gemini_load_chunk.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 755, in load | |
| extra_fields = gemini_loader.populate_from_vcf() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 176, in populate_from_vcf | |
| os.unlink(self.extra_vcf_writer.stream.name) | |
| OSError: [Errno 2] No such file or directory: '/tmp/extra.batch01-effects-ploidyfix.vcf.chunk4.db.vcf' | |
| Indexing /home/michael/Documents/projects/exon/scratch/vardict/batch01-effects-ploidyfix.vcf.gz with grabix. | |
| Loading 864377 variants. | |
| Breaking /home/michael/Documents/projects/exon/scratch/vardict/batch01-effects-ploidyfix.vcf.gz into 10 chunks. | |
| Loading chunk 0. | |
| Loading chunk 1. | |
| Loading chunk 2. | |
| Loading chunk 3. | |
| Loading chunk 4. | |
| Loading chunk 5. | |
| Loading chunk 6. | |
| Loading chunk 7. | |
| Loading chunk 8. | |
| Loading chunk 9. | |
| Traceback (most recent call last): | |
| File "/home/michael/bin/bcbionextgen/tools/bin/gemini", line 6, in <module> | |
| gemini.gemini_main.main() | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1121, in main | |
| args.func(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 196, in load_fn | |
| gemini_load.load(parser, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 50, in load | |
| load_multicore(args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 80, in load_multicore | |
| chunks = load_chunks_multicore(grabix_file, args) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 247, in load_chunks_multicore | |
| wait_until_finished(procs) | |
| File "/home/michael/bin/bcbionextgen/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 338, in wait_until_finished | |
| raise ValueError("Processing failed on GEMINI chunk load") | |
| ValueError: Processing failed on GEMINI chunk load | |
| ' returned non-zero exit status 1 | |
| [2015-06-29T12:46Z] Finalizing variant calls: Sample_AEXX, freebayes | |
| [2015-06-29T12:46Z] Calculating variation effects for Sample_AEXX, freebayes |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment