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biocyberman/bcbio_nextgen_debug.py

Created August 18, 2013 12:49
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bcbio_nextgen_debug.py
[2013-08-18 09:34] INFO 11:34:24,077 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:24,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:24,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:24,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:24,081 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpn8kdHQ/WES01_WES01_SQ1_FT2-chr19-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpn8kdHQ/WES01_WES01_SQ1_FT2-chr19-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:34] INFO 11:34:24,081 HelpFormatter - Date/Time: 2013/08/18 11:34:24
[2013-08-18 09:34] INFO 11:34:24,081 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:24,081 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:24,541 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:34] INFO 11:34:24,619 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:34] INFO 11:34:24,626 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:34] INFO 11:34:24,642 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2013-08-18 09:34] INFO 11:34:25,236 IntervalUtils - Processing 3585294 bp from intervals
[2013-08-18 09:34] INFO 11:34:25,308 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:34] INFO 11:34:25,571 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:34] INFO 11:34:25,572 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:34] INFO 11:34:25,573 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:34] INFO 11:34:26,566 ProgressMeter - done 6.13e+06 15.0 s 2.0 s 100.0% 15.0 s 0.0 s
[2013-08-18 09:34] INFO 11:34:26,567 ProgressMeter - Total runtime 15.03 secs, 0.25 min, 0.00 hours
[2013-08-18 09:34] INFO 11:34:26,567 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1282126 total reads (0.00%)
[2013-08-18 09:34] INFO 11:34:26,567 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:34] INFO 11:34:26,567 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:34] INFO 11:34:26,567 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:34] INFO 11:34:26,568 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:34] INFO 11:34:26,568 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:34] INFO 11:34:26,568 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:34] GATK: CallableLoci
[2013-08-18 09:34] INFO 11:34:27,502 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:34] INFO 11:34:29,128 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-split/tx/tmpumdISe/WES01_WES01_SQ2_FT1-chrX-callable-regions.bed to be BED
[2013-08-18 09:34] INFO 11:34:29,160 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:29,161 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:29,161 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:29,161 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:29,164 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1.bam --out /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-split/tx/tmpumdISe/WES01_WES01_SQ2_FT1-chrX-callable.bed --summary /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-split/tx/tmpumdISe/WES01_WES01_SQ2_FT1-chrX-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:34] INFO 11:34:29,165 HelpFormatter - Date/Time: 2013/08/18 11:34:29
[2013-08-18 09:34] INFO 11:34:29,165 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:29,165 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:29,616 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:34] INFO 11:34:29,694 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:34] INFO 11:34:29,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:34] INFO 11:34:29,717 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2013-08-18 09:34] INFO 11:34:29,968 IntervalUtils - Processing 2355594 bp from intervals
[2013-08-18 09:34] INFO 11:34:30,025 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:34] INFO 11:34:30,304 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:34] INFO 11:34:30,305 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:34] INFO 11:34:30,305 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:34] GATK: CallableLoci
[2013-08-18 09:34] INFO 11:34:33,028 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmp7B9Hjd/WES01_WES01_SQ1_Far-chr21-callable-regions.bed to be BED
[2013-08-18 09:34] INFO 11:34:33,059 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:33,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:33,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:33,059 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:33,062 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam --out /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmp7B9Hjd/WES01_WES01_SQ1_Far-chr21-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmp7B9Hjd/WES01_WES01_SQ1_Far-chr21-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:34] INFO 11:34:33,062 HelpFormatter - Date/Time: 2013/08/18 11:34:33
[2013-08-18 09:34] INFO 11:34:33,062 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:33,063 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:33,475 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:34] INFO 11:34:33,547 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:34] INFO 11:34:33,553 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:34] INFO 11:34:33,568 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:34] INFO 11:34:33,684 IntervalUtils - Processing 653506 bp from intervals
[2013-08-18 09:34] INFO 11:34:33,735 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:34] INFO 11:34:33,873 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:34] INFO 11:34:33,874 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:34] INFO 11:34:33,875 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:34] INFO 11:34:35,281 ProgressMeter - chr15:83088762 8.11e+06 30.0 s 3.0 s 81.5% 36.0 s 6.0 s
[2013-08-18 09:34] INFO 11:34:41,139 ProgressMeter - done 9.84e+06 35.0 s 3.0 s 100.0% 35.0 s 0.0 s
[2013-08-18 09:34] INFO 11:34:41,139 ProgressMeter - Total runtime 35.86 secs, 0.60 min, 0.01 hours
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3508673 total reads (0.00%)
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:34] INFO 11:34:41,140 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:34] INFO 11:34:41,955 ProgressMeter - done 2.27e+06 8.0 s 3.0 s 100.0% 8.0 s 0.0 s
[2013-08-18 09:34] INFO 11:34:41,955 ProgressMeter - Total runtime 8.08 secs, 0.13 min, 0.00 hours
[2013-08-18 09:34] INFO 11:34:41,956 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 638701 total reads (0.00%)
[2013-08-18 09:34] INFO 11:34:41,956 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:34] INFO 11:34:41,956 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:34] INFO 11:34:41,956 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:34] INFO 11:34:41,956 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:34] INFO 11:34:41,956 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:34] INFO 11:34:41,957 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:34] INFO 11:34:42,024 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:34] INFO 11:34:42,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:34] GATK: CallableLoci
[2013-08-18 09:34] GATK: CallableLoci
[2013-08-18 09:34] INFO 11:34:47,577 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpOVroiz/WES01_WES01_SQ1_Mor-chr16-callable-regions.bed to be BED
[2013-08-18 09:34] INFO 11:34:47,606 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:47,607 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:47,607 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:47,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:47,610 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpOVroiz/WES01_WES01_SQ1_Mor-chr16-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpOVroiz/WES01_WES01_SQ1_Mor-chr16-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:34] INFO 11:34:47,610 HelpFormatter - Date/Time: 2013/08/18 11:34:47
[2013-08-18 09:34] INFO 11:34:47,610 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:47,610 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:48,037 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:34] INFO 11:34:48,110 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:34] INFO 11:34:48,116 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:34] INFO 11:34:48,132 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:34] INFO 11:34:48,396 IntervalUtils - Processing 2613431 bp from intervals
[2013-08-18 09:34] INFO 11:34:48,438 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmp1Qs0n4/WES01_WES01_SQ1_Far-chr22-callable-regions.bed to be BED
[2013-08-18 09:34] INFO 11:34:48,449 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:34] INFO 11:34:48,468 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:48,469 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:48,469 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:48,469 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:48,472 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam --out /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmp1Qs0n4/WES01_WES01_SQ1_Far-chr22-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmp1Qs0n4/WES01_WES01_SQ1_Far-chr22-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:34] INFO 11:34:48,472 HelpFormatter - Date/Time: 2013/08/18 11:34:48
[2013-08-18 09:34] INFO 11:34:48,473 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:48,473 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:48,699 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:34] INFO 11:34:48,700 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:34] INFO 11:34:48,701 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:34] INFO 11:34:48,892 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:34] INFO 11:34:48,966 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:34] INFO 11:34:48,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:34] INFO 11:34:48,987 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:34] INFO 11:34:49,182 IntervalUtils - Processing 1373425 bp from intervals
[2013-08-18 09:34] INFO 11:34:49,234 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:34] INFO 11:34:49,402 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:34] INFO 11:34:49,403 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:34] INFO 11:34:49,403 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:34] INFO 11:34:55,577 ProgressMeter - chr19:51986533 1.43e+07 30.0 s 2.0 s 84.1% 35.0 s 5.0 s
[2013-08-18 09:34] GATK: BaseRecalibrator
[2013-08-18 09:34] INFO 11:34:59,504 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
[2013-08-18 09:34] INFO 11:34:59,548 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:59,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:59,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:59,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:59,552 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_Mor/tx/tmpHDDstz/WES01_WES01_SQ2_Mor.grp -I /data/proj01/work/prealign/WESF120601_B2_Mor/WES01_WES01_SQ2_Mor.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:34] INFO 11:34:59,552 HelpFormatter - Date/Time: 2013/08/18 11:34:59
[2013-08-18 09:34] INFO 11:34:59,552 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:59,552 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:59,560 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
[2013-08-18 09:34] INFO 11:34:59,974 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:00,047 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2013-08-18 09:35] INFO 11:35:00,053 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:00,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:35] INFO 11:35:00,081 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
[2013-08-18 09:35] INFO 11:35:00,312 ProgressMeter - chrX:153499116 8.14e+06 30.0 s 3.0 s 95.3% 31.0 s 1.0 s
[2013-08-18 09:35] INFO 11:35:01,738 ProgressMeter - done 8.68e+06 31.0 s 3.0 s 100.0% 31.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:01,738 ProgressMeter - Total runtime 31.43 secs, 0.52 min, 0.01 hours
[2013-08-18 09:35] INFO 11:35:01,738 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2930695 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:01,738 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:01,739 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:01,739 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:01,739 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:01,739 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:01,739 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] INFO 11:35:01,816 IntervalUtils - Processing 63564965 bp from intervals
[2013-08-18 09:35] INFO 11:35:02,019 ProgressMeter - done 1.63e+07 36.0 s 2.0 s 100.0% 36.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:02,020 ProgressMeter - Total runtime 36.45 secs, 0.61 min, 0.01 hours
[2013-08-18 09:35] INFO 11:35:02,020 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3413684 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:02,020 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:02,020 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:02,020 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:02,020 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:02,020 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:02,021 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] INFO 11:35:02,670 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] INFO 11:35:02,961 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] INFO 11:35:03,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:35] ##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
[2013-08-18 09:35] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
[2013-08-18 09:35] ##### ERROR Please do not post this error to the GATK forum
[2013-08-18 09:35] ##### ERROR
[2013-08-18 09:35] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
[2013-08-18 09:35] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2013-08-18 09:35] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
[2013-08-18 09:35] ##### ERROR
[2013-08-18 09:35] ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
[2013-08-18 09:35] ##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:35] ##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:35] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:35] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 46, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx2500m -Djava.io.tmpdir=/data/proj01/work/tmp/tmpYyxU2T -jar /opt/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_Mor/tx/tmpHDDstz/WES01_WES01_SQ2_Mor.grp -I /data/proj01/work/prealign/WESF120601_B2_Mor/WES01_WES01_SQ2_Mor.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:34:59,504 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
INFO 11:34:59,548 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:34:59,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
INFO 11:34:59,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:34:59,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:34:59,552 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_Mor/tx/tmpHDDstz/WES01_WES01_SQ2_Mor.grp -I /data/proj01/work/prealign/WESF120601_B2_Mor/WES01_WES01_SQ2_Mor.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:34:59,552 HelpFormatter - Date/Time: 2013/08/18 11:34:59
INFO 11:34:59,552 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:34:59,552 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:34:59,560 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
INFO 11:34:59,974 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:35:00,047 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:35:00,053 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:35:00,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:35:00,081 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
INFO 11:35:01,816 IntervalUtils - Processing 63564965 bp from intervals
INFO 11:35:03,112 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
[2013-08-18 09:35] INFO 11:35:05,257 ProgressMeter - done 5.82e+06 15.0 s 2.0 s 100.0% 15.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:05,257 ProgressMeter - Total runtime 15.85 secs, 0.26 min, 0.00 hours
[2013-08-18 09:35] INFO 11:35:05,258 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1400533 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:05,258 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:05,258 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:05,258 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:05,258 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:05,258 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:05,259 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:06,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:08,560 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-split/tx/tmpKBdxHp/WES01_WES01_SQ2_FT1-chrY-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:08,593 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:08,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:08,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:08,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:08,597 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1.bam --out /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-split/tx/tmpKBdxHp/WES01_WES01_SQ2_FT1-chrY-callable.bed --summary /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1-callable-split/tx/tmpKBdxHp/WES01_WES01_SQ2_FT1-chrY-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:08,597 HelpFormatter - Date/Time: 2013/08/18 11:35:08
[2013-08-18 09:35] INFO 11:35:08,597 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:08,597 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:08,871 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpcEB2c1/WES01_WES01_SQ1_FT2-chr20-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:08,903 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:08,904 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:08,904 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:08,904 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:08,908 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpcEB2c1/WES01_WES01_SQ1_FT2-chr20-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpcEB2c1/WES01_WES01_SQ1_FT2-chr20-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:08,908 HelpFormatter - Date/Time: 2013/08/18 11:35:08
[2013-08-18 09:35] INFO 11:35:08,908 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:08,908 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:09,055 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:09,129 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:09,136 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:09,151 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:35] INFO 11:35:09,217 IntervalUtils - Processing 219372 bp from intervals
[2013-08-18 09:35] INFO 11:35:09,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] INFO 11:35:09,360 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:09,368 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:09,369 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:09,369 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:35] INFO 11:35:09,436 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:09,442 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:09,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:09,661 IntervalUtils - Processing 1478124 bp from intervals
[2013-08-18 09:35] INFO 11:35:09,718 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] INFO 11:35:09,905 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:09,906 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:09,906 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:35] INFO 11:35:11,758 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmpKtXUMQ/WES01_WES01_SQ1_Far-chrX-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:11,786 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:11,786 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:11,786 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:11,787 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:11,790 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam --out /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmpKtXUMQ/WES01_WES01_SQ1_Far-chrX-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmpKtXUMQ/WES01_WES01_SQ1_Far-chrX-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:11,790 HelpFormatter - Date/Time: 2013/08/18 11:35:11
[2013-08-18 09:35] INFO 11:35:11,790 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:11,790 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:12,122 ProgressMeter - done 6.91e+05 2.0 s 3.0 s 100.0% 2.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:12,123 ProgressMeter - Total runtime 2.75 secs, 0.05 min, 0.00 hours
[2013-08-18 09:35] INFO 11:35:12,123 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 132643 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:12,123 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:12,124 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:12,124 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:12,124 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:12,124 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:12,125 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] INFO 11:35:12,208 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:12,278 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:12,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:12,301 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2013-08-18 09:35] INFO 11:35:12,547 IntervalUtils - Processing 2355594 bp from intervals
[2013-08-18 09:35] INFO 11:35:12,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] INFO 11:35:12,883 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:12,884 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:12,884 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:35] INFO 11:35:13,010 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] multiprocessing: combine_bed
[2013-08-18 09:35] INFO 11:35:18,708 ProgressMeter - chr16:67268306 1.00e+07 30.0 s 2.0 s 72.4% 41.0 s 11.0 s
[2013-08-18 09:35] INFO 11:35:26,051 ProgressMeter - done 6.13e+06 16.0 s 2.0 s 100.0% 16.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:26,051 ProgressMeter - Total runtime 16.15 secs, 0.27 min, 0.00 hours
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1393869 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:26,052 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] INFO 11:35:26,963 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] INFO 11:35:28,664 ProgressMeter - done 1.33e+07 39.0 s 2.0 s 100.0% 39.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:28,665 ProgressMeter - Total runtime 39.96 secs, 0.67 min, 0.01 hours
[2013-08-18 09:35] INFO 11:35:28,665 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3896967 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:28,665 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:28,665 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:28,665 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:28,665 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:28,666 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:28,666 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:29,958 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] INFO 11:35:32,139 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmp2ZgdyZ/WES01_WES01_SQ1_FT2-chr21-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:32,172 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:32,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:32,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:32,172 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:32,176 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmp2ZgdyZ/WES01_WES01_SQ1_FT2-chr21-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmp2ZgdyZ/WES01_WES01_SQ1_FT2-chr21-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:32,176 HelpFormatter - Date/Time: 2013/08/18 11:35:32
[2013-08-18 09:35] INFO 11:35:32,176 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:32,176 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:32,664 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:32,737 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:32,744 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:32,759 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:35] INFO 11:35:32,884 IntervalUtils - Processing 653506 bp from intervals
[2013-08-18 09:35] INFO 11:35:32,939 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:33,079 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:33,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:33,080 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:35] INFO 11:35:33,551 ProgressMeter - done 8.68e+06 20.0 s 2.0 s 100.0% 20.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:33,551 ProgressMeter - Total runtime 20.67 secs, 0.34 min, 0.01 hours
[2013-08-18 09:35] INFO 11:35:33,552 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1665331 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:33,552 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:33,552 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:33,552 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:33,552 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:33,552 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:33,553 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] Recalibrating ('', 'WESF120601_B2_FT1') with GATK
[2013-08-18 09:35] INFO 11:35:34,434 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] INFO 11:35:35,165 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmp922VfV/WES01_WES01_SQ1_Mor-chr17-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:35,200 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:35,200 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:35,201 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:35,201 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:35,205 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmp922VfV/WES01_WES01_SQ1_Mor-chr17-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmp922VfV/WES01_WES01_SQ1_Mor-chr17-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:35,205 HelpFormatter - Date/Time: 2013/08/18 11:35:35
[2013-08-18 09:35] INFO 11:35:35,205 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:35,205 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:35,656 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:35,731 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:35,738 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:35,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:35] INFO 11:35:36,071 IntervalUtils - Processing 3437731 bp from intervals
[2013-08-18 09:35] INFO 11:35:36,167 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] INFO 11:35:36,405 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:36,405 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:36,406 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:39,650 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmpby80RK/WES01_WES01_SQ1_Far-chrY-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:39,680 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:39,680 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:39,681 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:39,681 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:39,684 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam --out /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmpby80RK/WES01_WES01_SQ1_Far-chrY-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far-callable-split/tx/tmpby80RK/WES01_WES01_SQ1_Far-chrY-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:39,684 HelpFormatter - Date/Time: 2013/08/18 11:35:39
[2013-08-18 09:35] INFO 11:35:39,684 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:39,684 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:40,114 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:40,186 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:40,193 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:40,208 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:35] INFO 11:35:40,272 IntervalUtils - Processing 219372 bp from intervals
[2013-08-18 09:35] INFO 11:35:40,321 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] INFO 11:35:40,430 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:40,431 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:40,431 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:35] INFO 11:35:42,015 ProgressMeter - done 2.27e+06 8.0 s 3.0 s 100.0% 8.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:42,015 ProgressMeter - Total runtime 8.94 secs, 0.15 min, 0.00 hours
[2013-08-18 09:35] INFO 11:35:42,015 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 728913 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:42,015 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:42,016 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:42,016 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:42,016 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:42,016 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:42,016 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] INFO 11:35:42,917 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] GATK: CallableLoci
[2013-08-18 09:35] INFO 11:35:46,449 ProgressMeter - done 6.91e+05 6.0 s 8.0 s 100.0% 6.0 s 0.0 s
[2013-08-18 09:35] INFO 11:35:46,449 ProgressMeter - Total runtime 6.02 secs, 0.10 min, 0.00 hours
[2013-08-18 09:35] INFO 11:35:46,449 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 471214 total reads (0.00%)
[2013-08-18 09:35] INFO 11:35:46,449 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:35] INFO 11:35:46,450 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:35] INFO 11:35:46,450 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:35] INFO 11:35:46,450 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:35] INFO 11:35:46,450 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:35] INFO 11:35:46,450 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:35] INFO 11:35:47,405 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:35] multiprocessing: combine_bed
[2013-08-18 09:35] INFO 11:35:47,922 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpi6GM6T/WES01_WES01_SQ1_FT2-chr22-callable-regions.bed to be BED
[2013-08-18 09:35] INFO 11:35:47,951 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:47,951 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:35] INFO 11:35:47,951 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:35] INFO 11:35:47,951 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:35] INFO 11:35:47,954 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpi6GM6T/WES01_WES01_SQ1_FT2-chr22-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpi6GM6T/WES01_WES01_SQ1_FT2-chr22-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:35] INFO 11:35:47,954 HelpFormatter - Date/Time: 2013/08/18 11:35:47
[2013-08-18 09:35] INFO 11:35:47,954 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:47,955 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:35] INFO 11:35:48,403 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:35] INFO 11:35:48,473 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:35] INFO 11:35:48,479 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:35] INFO 11:35:48,493 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:35] INFO 11:35:48,678 IntervalUtils - Processing 1373425 bp from intervals
[2013-08-18 09:35] INFO 11:35:48,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:35] INFO 11:35:48,901 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:35] INFO 11:35:48,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:35] INFO 11:35:48,902 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:36] INFO 11:36:05,532 ProgressMeter - done 5.82e+06 16.0 s 2.0 s 100.0% 16.0 s 0.0 s
[2013-08-18 09:36] INFO 11:36:05,532 ProgressMeter - Total runtime 16.63 secs, 0.28 min, 0.00 hours
[2013-08-18 09:36] INFO 11:36:05,532 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1582309 total reads (0.00%)
[2013-08-18 09:36] INFO 11:36:05,532 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:36] INFO 11:36:05,533 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:36] INFO 11:36:05,533 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:36] INFO 11:36:05,533 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:36] INFO 11:36:05,533 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:36] INFO 11:36:05,533 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:36] INFO 11:36:06,410 ProgressMeter - chr17:47036112 1.16e+07 30.0 s 2.0 s 64.1% 46.0 s 16.0 s
[2013-08-18 09:36] INFO 11:36:06,597 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:36] Recalibrating ('', 'WESF120601_B1_Far') with GATK
[2013-08-18 09:36] GATK: CallableLoci
[2013-08-18 09:36] INFO 11:36:11,863 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpWXiVLG/WES01_WES01_SQ1_FT2-chrX-callable-regions.bed to be BED
[2013-08-18 09:36] INFO 11:36:11,935 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:11,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:36] INFO 11:36:11,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:36] INFO 11:36:11,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:36] INFO 11:36:11,943 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpWXiVLG/WES01_WES01_SQ1_FT2-chrX-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpWXiVLG/WES01_WES01_SQ1_FT2-chrX-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:36] INFO 11:36:11,944 HelpFormatter - Date/Time: 2013/08/18 11:36:11
[2013-08-18 09:36] INFO 11:36:11,944 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:11,944 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:12,573 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:36] INFO 11:36:12,645 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:36] INFO 11:36:12,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:36] INFO 11:36:12,667 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:36] INFO 11:36:12,923 IntervalUtils - Processing 2355594 bp from intervals
[2013-08-18 09:36] INFO 11:36:12,977 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:36] INFO 11:36:13,271 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:36] INFO 11:36:13,272 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:36] INFO 11:36:13,273 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:36] INFO 11:36:20,880 ProgressMeter - done 1.81e+07 44.0 s 2.0 s 100.0% 44.0 s 0.0 s
[2013-08-18 09:36] INFO 11:36:20,881 ProgressMeter - Total runtime 44.48 secs, 0.74 min, 0.01 hours
[2013-08-18 09:36] INFO 11:36:20,881 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 4541620 total reads (0.00%)
[2013-08-18 09:36] INFO 11:36:20,881 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:36] INFO 11:36:20,881 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:36] INFO 11:36:20,881 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:36] INFO 11:36:20,881 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:36] INFO 11:36:20,882 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:36] INFO 11:36:20,882 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:36] INFO 11:36:22,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:36] GATK: CallableLoci
[2013-08-18 09:36] INFO 11:36:29,247 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmplrvJIM/WES01_WES01_SQ1_Mor-chr18-callable-regions.bed to be BED
[2013-08-18 09:36] INFO 11:36:29,273 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:29,273 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:36] INFO 11:36:29,273 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:36] INFO 11:36:29,273 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:36] INFO 11:36:29,277 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmplrvJIM/WES01_WES01_SQ1_Mor-chr18-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmplrvJIM/WES01_WES01_SQ1_Mor-chr18-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:36] INFO 11:36:29,277 HelpFormatter - Date/Time: 2013/08/18 11:36:29
[2013-08-18 09:36] INFO 11:36:29,277 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:29,277 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:29,689 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:36] INFO 11:36:29,773 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:36] INFO 11:36:29,780 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:36] INFO 11:36:29,795 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:36] INFO 11:36:29,938 IntervalUtils - Processing 912353 bp from intervals
[2013-08-18 09:36] INFO 11:36:29,990 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:36] INFO 11:36:30,163 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:36] INFO 11:36:30,163 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:36] INFO 11:36:30,164 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:36] INFO 11:36:43,278 ProgressMeter - chrX:129338809 6.50e+06 30.0 s 4.0 s 78.0% 38.0 s 8.0 s
[2013-08-18 09:36] INFO 11:36:44,097 ProgressMeter - done 2.64e+06 13.0 s 5.0 s 100.0% 13.0 s 0.0 s
[2013-08-18 09:36] INFO 11:36:44,097 ProgressMeter - Total runtime 13.93 secs, 0.23 min, 0.00 hours
[2013-08-18 09:36] INFO 11:36:44,097 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1235692 total reads (0.00%)
[2013-08-18 09:36] INFO 11:36:44,097 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:36] INFO 11:36:44,097 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:36] INFO 11:36:44,098 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:36] INFO 11:36:44,098 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:36] INFO 11:36:44,098 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:36] INFO 11:36:44,098 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:36] INFO 11:36:45,044 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:36] INFO 11:36:51,371 ProgressMeter - done 8.69e+06 38.0 s 4.0 s 100.0% 38.0 s 0.0 s
[2013-08-18 09:36] INFO 11:36:51,372 ProgressMeter - Total runtime 38.10 secs, 0.63 min, 0.01 hours
[2013-08-18 09:36] INFO 11:36:51,372 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3799283 total reads (0.00%)
[2013-08-18 09:36] INFO 11:36:51,372 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:36] INFO 11:36:51,372 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:36] INFO 11:36:51,372 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:36] INFO 11:36:51,372 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:36] INFO 11:36:51,373 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:36] INFO 11:36:51,373 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:36] GATK: CallableLoci
[2013-08-18 09:36] INFO 11:36:52,557 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:36] INFO 11:36:55,488 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpdDC7nH/WES01_WES01_SQ1_Mor-chr19-callable-regions.bed to be BED
[2013-08-18 09:36] INFO 11:36:55,519 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:55,520 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:36] INFO 11:36:55,520 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:36] INFO 11:36:55,520 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:36] INFO 11:36:55,523 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpdDC7nH/WES01_WES01_SQ1_Mor-chr19-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpdDC7nH/WES01_WES01_SQ1_Mor-chr19-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:36] INFO 11:36:55,524 HelpFormatter - Date/Time: 2013/08/18 11:36:55
[2013-08-18 09:36] INFO 11:36:55,524 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:55,524 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:55,976 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:36] INFO 11:36:56,063 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:36] INFO 11:36:56,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:36] INFO 11:36:56,084 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:36] GATK: CallableLoci
[2013-08-18 09:36] INFO 11:36:56,381 IntervalUtils - Processing 3585294 bp from intervals
[2013-08-18 09:36] INFO 11:36:56,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:36] INFO 11:36:56,682 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:36] INFO 11:36:56,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:36] INFO 11:36:56,683 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:36] INFO 11:36:59,222 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpd4KqhW/WES01_WES01_SQ1_FT2-chrY-callable-regions.bed to be BED
[2013-08-18 09:36] INFO 11:36:59,261 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:59,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:36] INFO 11:36:59,262 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:36] INFO 11:36:59,262 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:36] INFO 11:36:59,266 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpd4KqhW/WES01_WES01_SQ1_FT2-chrY-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpd4KqhW/WES01_WES01_SQ1_FT2-chrY-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:36] INFO 11:36:59,266 HelpFormatter - Date/Time: 2013/08/18 11:36:59
[2013-08-18 09:36] INFO 11:36:59,266 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:59,266 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:36] INFO 11:36:59,657 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:36] INFO 11:36:59,724 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:36] INFO 11:36:59,730 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:36] INFO 11:36:59,743 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:36] INFO 11:36:59,875 IntervalUtils - Processing 219372 bp from intervals
[2013-08-18 09:37] INFO 11:37:00,003 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:37] INFO 11:37:00,267 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:37] INFO 11:37:00,268 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:37] INFO 11:37:00,269 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:37] INFO 11:37:02,921 ProgressMeter - done 6.97e+05 2.0 s 3.0 s 100.0% 2.0 s 0.0 s
[2013-08-18 09:37] INFO 11:37:02,921 ProgressMeter - Total runtime 2.65 secs, 0.04 min, 0.00 hours
[2013-08-18 09:37] INFO 11:37:02,921 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 145486 total reads (0.00%)
[2013-08-18 09:37] INFO 11:37:02,922 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:37] INFO 11:37:02,922 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:37] INFO 11:37:02,922 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:37] INFO 11:37:02,922 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:37] INFO 11:37:02,922 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:37] INFO 11:37:02,922 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:37] INFO 11:37:03,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:37] multiprocessing: combine_bed
[2013-08-18 09:37] GATK: BaseRecalibrator
[2013-08-18 09:37] INFO 11:37:16,876 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
[2013-08-18 09:37] INFO 11:37:16,917 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:37] INFO 11:37:16,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:37] INFO 11:37:16,918 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:37] INFO 11:37:16,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:37] INFO 11:37:16,921 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_FT2/tx/tmpG0I3HW/WES01_WES01_SQ2_FT2.grp -I /data/proj01/work/prealign/WESF120601_B2_FT2/WES01_WES01_SQ2_FT2.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:37] INFO 11:37:16,921 HelpFormatter - Date/Time: 2013/08/18 11:37:16
[2013-08-18 09:37] INFO 11:37:16,921 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:37] INFO 11:37:16,921 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:37] INFO 11:37:16,929 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
[2013-08-18 09:37] INFO 11:37:17,330 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:37] INFO 11:37:17,396 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2013-08-18 09:37] INFO 11:37:17,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:37] INFO 11:37:17,415 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:37] INFO 11:37:17,427 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
[2013-08-18 09:37] INFO 11:37:19,001 IntervalUtils - Processing 63564965 bp from intervals
[2013-08-18 09:37] INFO 11:37:20,151 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:37] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:37] ##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
[2013-08-18 09:37] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
[2013-08-18 09:37] ##### ERROR Please do not post this error to the GATK forum
[2013-08-18 09:37] ##### ERROR
[2013-08-18 09:37] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
[2013-08-18 09:37] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2013-08-18 09:37] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
[2013-08-18 09:37] ##### ERROR
[2013-08-18 09:37] ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
[2013-08-18 09:37] ##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:37] ##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:37] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:37] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 46, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx2500m -Djava.io.tmpdir=/data/proj01/work/tmp/tmp1EnM5i -jar /opt/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_FT2/tx/tmpG0I3HW/WES01_WES01_SQ2_FT2.grp -I /data/proj01/work/prealign/WESF120601_B2_FT2/WES01_WES01_SQ2_FT2.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:37:16,876 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
INFO 11:37:16,917 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:37:16,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
INFO 11:37:16,918 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:37:16,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:37:16,921 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_FT2/tx/tmpG0I3HW/WES01_WES01_SQ2_FT2.grp -I /data/proj01/work/prealign/WESF120601_B2_FT2/WES01_WES01_SQ2_FT2.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:37:16,921 HelpFormatter - Date/Time: 2013/08/18 11:37:16
INFO 11:37:16,921 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:37:16,921 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:37:16,929 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
INFO 11:37:17,330 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:37:17,396 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:37:17,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:37:17,415 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:37:17,427 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
INFO 11:37:19,001 IntervalUtils - Processing 63564965 bp from intervals
INFO 11:37:20,151 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
[2013-08-18 09:37] Recalibrating ('', 'WESF120601_B1_FT2') with GATK
[2013-08-18 09:37] INFO 11:37:26,693 ProgressMeter - chr19:46025459 1.20e+07 30.0 s 2.0 s 70.4% 42.0 s 12.0 s
[2013-08-18 09:37] INFO 11:37:38,963 ProgressMeter - done 1.63e+07 42.0 s 2.0 s 100.0% 42.0 s 0.0 s
[2013-08-18 09:37] INFO 11:37:38,964 ProgressMeter - Total runtime 42.28 secs, 0.70 min, 0.01 hours
[2013-08-18 09:37] INFO 11:37:38,964 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 4111773 total reads (0.00%)
[2013-08-18 09:37] INFO 11:37:38,964 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:37] INFO 11:37:38,964 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:37] INFO 11:37:38,964 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:37] INFO 11:37:38,964 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:37] INFO 11:37:38,965 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:37] INFO 11:37:38,965 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:37] INFO 11:37:40,311 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:37] GATK: CallableLoci
[2013-08-18 09:37] INFO 11:37:50,640 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpn2aVSb/WES01_WES01_SQ1_Mor-chr20-callable-regions.bed to be BED
[2013-08-18 09:37] INFO 11:37:50,666 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:37] INFO 11:37:50,667 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:37] INFO 11:37:50,667 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:37] INFO 11:37:50,667 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:37] INFO 11:37:50,670 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpn2aVSb/WES01_WES01_SQ1_Mor-chr20-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpn2aVSb/WES01_WES01_SQ1_Mor-chr20-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:37] INFO 11:37:50,670 HelpFormatter - Date/Time: 2013/08/18 11:37:50
[2013-08-18 09:37] INFO 11:37:50,670 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:37] INFO 11:37:50,670 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:37] INFO 11:37:51,067 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:37] INFO 11:37:51,133 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:37] INFO 11:37:51,139 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:37] INFO 11:37:51,153 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:37] INFO 11:37:51,334 IntervalUtils - Processing 1478124 bp from intervals
[2013-08-18 09:37] INFO 11:37:51,381 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:37] INFO 11:37:51,554 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:37] INFO 11:37:51,555 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:37] INFO 11:37:51,555 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:38] INFO 11:38:09,237 ProgressMeter - done 6.13e+06 17.0 s 2.0 s 100.0% 17.0 s 0.0 s
[2013-08-18 09:38] INFO 11:38:09,237 ProgressMeter - Total runtime 17.68 secs, 0.29 min, 0.00 hours
[2013-08-18 09:38] INFO 11:38:09,237 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1799195 total reads (0.00%)
[2013-08-18 09:38] INFO 11:38:09,238 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:38] INFO 11:38:09,238 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:38] INFO 11:38:09,238 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:38] INFO 11:38:09,238 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:38] INFO 11:38:09,238 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:38] INFO 11:38:09,238 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:38] INFO 11:38:10,088 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:38] GATK: CallableLoci
[2013-08-18 09:38] INFO 11:38:19,837 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmplbP9Eo/WES01_WES01_SQ1_Mor-chr21-callable-regions.bed to be BED
[2013-08-18 09:38] INFO 11:38:19,864 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:38] INFO 11:38:19,864 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:38] INFO 11:38:19,864 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:38] INFO 11:38:19,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:38] INFO 11:38:19,867 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmplbP9Eo/WES01_WES01_SQ1_Mor-chr21-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmplbP9Eo/WES01_WES01_SQ1_Mor-chr21-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:38] INFO 11:38:19,867 HelpFormatter - Date/Time: 2013/08/18 11:38:19
[2013-08-18 09:38] INFO 11:38:19,867 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:38] INFO 11:38:19,867 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:38] INFO 11:38:20,304 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:38] INFO 11:38:20,507 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:38] INFO 11:38:20,523 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:38] INFO 11:38:20,561 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2013-08-18 09:38] INFO 11:38:20,877 IntervalUtils - Processing 653506 bp from intervals
[2013-08-18 09:38] INFO 11:38:21,008 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:38] INFO 11:38:21,305 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:38] INFO 11:38:21,305 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:38] INFO 11:38:21,306 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:38] INFO 11:38:30,961 ProgressMeter - done 2.27e+06 9.0 s 4.0 s 100.0% 9.0 s 0.0 s
[2013-08-18 09:38] INFO 11:38:30,961 ProgressMeter - Total runtime 9.66 secs, 0.16 min, 0.00 hours
[2013-08-18 09:38] INFO 11:38:30,961 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 922280 total reads (0.00%)
[2013-08-18 09:38] INFO 11:38:30,961 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:38] INFO 11:38:30,961 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:38] INFO 11:38:30,962 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:38] INFO 11:38:30,962 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:38] INFO 11:38:30,962 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:38] INFO 11:38:30,962 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:38] INFO 11:38:31,923 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:38] GATK: CallableLoci
[2013-08-18 09:38] INFO 11:38:41,536 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpUHcf7F/WES01_WES01_SQ1_Mor-chr22-callable-regions.bed to be BED
[2013-08-18 09:38] INFO 11:38:41,563 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:38] INFO 11:38:41,563 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:38] INFO 11:38:41,563 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:38] INFO 11:38:41,563 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:38] INFO 11:38:41,566 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpUHcf7F/WES01_WES01_SQ1_Mor-chr22-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpUHcf7F/WES01_WES01_SQ1_Mor-chr22-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:38] INFO 11:38:41,566 HelpFormatter - Date/Time: 2013/08/18 11:38:41
[2013-08-18 09:38] INFO 11:38:41,566 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:38] INFO 11:38:41,566 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:38] INFO 11:38:41,993 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:38] INFO 11:38:42,085 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:38] INFO 11:38:42,093 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:38] INFO 11:38:42,110 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2013-08-18 09:38] INFO 11:38:42,318 IntervalUtils - Processing 1373425 bp from intervals
[2013-08-18 09:38] INFO 11:38:42,366 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:38] INFO 11:38:42,531 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:38] INFO 11:38:42,532 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:38] INFO 11:38:42,532 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:39] INFO 11:39:00,497 ProgressMeter - done 5.82e+06 17.0 s 3.0 s 100.0% 17.0 s 0.0 s
[2013-08-18 09:39] INFO 11:39:00,497 ProgressMeter - Total runtime 17.97 secs, 0.30 min, 0.00 hours
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1871724 total reads (0.00%)
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:39] INFO 11:39:00,498 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:39] INFO 11:39:01,677 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:39] GATK: CallableLoci
[2013-08-18 09:39] INFO 11:39:11,346 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpsi7_hU/WES01_WES01_SQ1_Mor-chrX-callable-regions.bed to be BED
[2013-08-18 09:39] INFO 11:39:11,372 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:39] INFO 11:39:11,372 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:39] INFO 11:39:11,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:39] INFO 11:39:11,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:39] INFO 11:39:11,375 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpsi7_hU/WES01_WES01_SQ1_Mor-chrX-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpsi7_hU/WES01_WES01_SQ1_Mor-chrX-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:39] INFO 11:39:11,376 HelpFormatter - Date/Time: 2013/08/18 11:39:11
[2013-08-18 09:39] INFO 11:39:11,376 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:39] INFO 11:39:11,376 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:39] INFO 11:39:11,757 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:39] INFO 11:39:11,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:39] INFO 11:39:11,962 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:39] INFO 11:39:12,001 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2013-08-18 09:39] INFO 11:39:12,638 IntervalUtils - Processing 2355594 bp from intervals
[2013-08-18 09:39] INFO 11:39:12,770 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:39] INFO 11:39:13,021 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:39] INFO 11:39:13,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:39] INFO 11:39:13,022 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:39] INFO 11:39:43,030 ProgressMeter - chrX:101478986 5.05e+06 30.0 s 5.0 s 58.8% 51.0 s 21.0 s
[2013-08-18 09:40] INFO 11:40:01,563 ProgressMeter - done 8.68e+06 48.0 s 5.0 s 100.0% 48.0 s 0.0 s
[2013-08-18 09:40] INFO 11:40:01,564 ProgressMeter - Total runtime 48.54 secs, 0.81 min, 0.01 hours
[2013-08-18 09:40] INFO 11:40:01,564 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 4750865 total reads (0.00%)
[2013-08-18 09:40] INFO 11:40:01,564 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:40] INFO 11:40:01,564 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:40] INFO 11:40:01,564 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:40] INFO 11:40:01,565 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:40] INFO 11:40:01,565 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:40] INFO 11:40:01,565 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:40] INFO 11:40:03,695 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:40] GATK: CallableLoci
[2013-08-18 09:40] INFO 11:40:12,461 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpRs7vRB/WES01_WES01_SQ1_Mor-chrY-callable-regions.bed to be BED
[2013-08-18 09:40] INFO 11:40:12,488 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:40] INFO 11:40:12,488 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:40] INFO 11:40:12,488 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:40] INFO 11:40:12,488 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:40] INFO 11:40:12,491 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam --out /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpRs7vRB/WES01_WES01_SQ1_Mor-chrY-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor-callable-split/tx/tmpRs7vRB/WES01_WES01_SQ1_Mor-chrY-callable-regions.bed -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:40] INFO 11:40:12,491 HelpFormatter - Date/Time: 2013/08/18 11:40:12
[2013-08-18 09:40] INFO 11:40:12,492 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:40] INFO 11:40:12,492 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:40] INFO 11:40:12,901 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:40] INFO 11:40:12,972 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2013-08-18 09:40] INFO 11:40:12,978 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:40] INFO 11:40:12,992 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:40] INFO 11:40:13,053 IntervalUtils - Processing 219372 bp from intervals
[2013-08-18 09:40] INFO 11:40:13,099 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2013-08-18 09:40] INFO 11:40:13,202 GenomeAnalysisEngine - Done preparing for traversal
[2013-08-18 09:40] INFO 11:40:13,203 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2013-08-18 09:40] INFO 11:40:13,203 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
[2013-08-18 09:40] INFO 11:40:16,188 ProgressMeter - done 6.92e+05 2.0 s 4.0 s 100.0% 2.0 s 0.0 s
[2013-08-18 09:40] INFO 11:40:16,188 ProgressMeter - Total runtime 2.98 secs, 0.05 min, 0.00 hours
[2013-08-18 09:40] INFO 11:40:16,188 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 165869 total reads (0.00%)
[2013-08-18 09:40] INFO 11:40:16,188 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
[2013-08-18 09:40] INFO 11:40:16,188 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2013-08-18 09:40] INFO 11:40:16,189 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2013-08-18 09:40] INFO 11:40:16,189 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
[2013-08-18 09:40] INFO 11:40:16,189 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2013-08-18 09:40] INFO 11:40:16,189 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2013-08-18 09:40] INFO 11:40:17,097 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:40] multiprocessing: combine_bed
[2013-08-18 09:40] Recalibrating ('', 'WESF120601_B1_Mor') with GATK
[2013-08-18 09:44] GATK: BaseRecalibrator
[2013-08-18 09:44] INFO 11:44:06,013 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
[2013-08-18 09:44] INFO 11:44:06,054 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:44] INFO 11:44:06,054 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:44] INFO 11:44:06,054 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:44] INFO 11:44:06,054 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:44] INFO 11:44:06,058 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_FT1/tx/tmpIwRkIu/WES01_WES01_SQ2_FT1.grp -I /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:44] INFO 11:44:06,058 HelpFormatter - Date/Time: 2013/08/18 11:44:06
[2013-08-18 09:44] INFO 11:44:06,058 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:44] INFO 11:44:06,058 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:44] INFO 11:44:06,065 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
[2013-08-18 09:44] INFO 11:44:06,502 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:44] INFO 11:44:06,615 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2013-08-18 09:44] INFO 11:44:06,621 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:44] INFO 11:44:06,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:44] INFO 11:44:06,647 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
[2013-08-18 09:44] INFO 11:44:08,379 IntervalUtils - Processing 63564965 bp from intervals
[2013-08-18 09:44] INFO 11:44:10,625 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:44] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:44] ##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
[2013-08-18 09:44] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
[2013-08-18 09:44] ##### ERROR Please do not post this error to the GATK forum
[2013-08-18 09:44] ##### ERROR
[2013-08-18 09:44] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
[2013-08-18 09:44] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2013-08-18 09:44] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
[2013-08-18 09:44] ##### ERROR
[2013-08-18 09:44] ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
[2013-08-18 09:44] ##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:44] ##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:44] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:44] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 46, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx2500m -Djava.io.tmpdir=/data/proj01/work/tmp/tmpsE11ZB -jar /opt/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_FT1/tx/tmpIwRkIu/WES01_WES01_SQ2_FT1.grp -I /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:44:06,013 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
INFO 11:44:06,054 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:44:06,054 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
INFO 11:44:06,054 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:44:06,054 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:44:06,058 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B2_FT1/tx/tmpIwRkIu/WES01_WES01_SQ2_FT1.grp -I /data/proj01/work/prealign/WESF120601_B2_FT1/WES01_WES01_SQ2_FT1.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:44:06,058 HelpFormatter - Date/Time: 2013/08/18 11:44:06
INFO 11:44:06,058 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:44:06,058 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:44:06,065 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
INFO 11:44:06,502 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:44:06,615 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:44:06,621 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:44:06,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:44:06,647 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
INFO 11:44:08,379 IntervalUtils - Processing 63564965 bp from intervals
INFO 11:44:10,625 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
[2013-08-18 09:45] GATK: BaseRecalibrator
[2013-08-18 09:45] INFO 11:45:10,195 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
[2013-08-18 09:45] INFO 11:45:10,238 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:45] INFO 11:45:10,238 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:45] INFO 11:45:10,238 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:45] INFO 11:45:10,238 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:45] INFO 11:45:10,241 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_Far/tx/tmpTxZkjt/WES01_WES01_SQ1_Far.grp -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:45] INFO 11:45:10,241 HelpFormatter - Date/Time: 2013/08/18 11:45:10
[2013-08-18 09:45] INFO 11:45:10,242 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:45] INFO 11:45:10,242 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:45] INFO 11:45:10,249 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
[2013-08-18 09:45] INFO 11:45:10,661 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:45] INFO 11:45:10,728 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2013-08-18 09:45] INFO 11:45:10,735 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:45] INFO 11:45:10,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:45] INFO 11:45:10,762 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
[2013-08-18 09:45] INFO 11:45:12,455 IntervalUtils - Processing 63564965 bp from intervals
[2013-08-18 09:45] INFO 11:45:14,186 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:45] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:45] ##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
[2013-08-18 09:45] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
[2013-08-18 09:45] ##### ERROR Please do not post this error to the GATK forum
[2013-08-18 09:45] ##### ERROR
[2013-08-18 09:45] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
[2013-08-18 09:45] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2013-08-18 09:45] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
[2013-08-18 09:45] ##### ERROR
[2013-08-18 09:45] ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
[2013-08-18 09:45] ##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:45] ##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:45] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:45] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 46, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx2500m -Djava.io.tmpdir=/data/proj01/work/tmp/tmpYln1jQ -jar /opt/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_Far/tx/tmpTxZkjt/WES01_WES01_SQ1_Far.grp -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:45:10,195 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
INFO 11:45:10,238 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:45:10,238 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
INFO 11:45:10,238 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:45:10,238 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:45:10,241 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_Far/tx/tmpTxZkjt/WES01_WES01_SQ1_Far.grp -I /data/proj01/work/prealign/WESF120601_B1_Far/WES01_WES01_SQ1_Far.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:45:10,241 HelpFormatter - Date/Time: 2013/08/18 11:45:10
INFO 11:45:10,242 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:45:10,242 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:45:10,249 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
INFO 11:45:10,661 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:45:10,728 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:45:10,735 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:45:10,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:45:10,762 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
INFO 11:45:12,455 IntervalUtils - Processing 63564965 bp from intervals
INFO 11:45:14,186 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
[2013-08-18 09:46] GATK: BaseRecalibrator
[2013-08-18 09:46] INFO 11:46:48,623 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
[2013-08-18 09:46] INFO 11:46:48,665 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:46] INFO 11:46:48,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:46] INFO 11:46:48,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:46] INFO 11:46:48,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:46] INFO 11:46:48,668 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_FT2/tx/tmpo4r4mz/WES01_WES01_SQ1_FT2.grp -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:46] INFO 11:46:48,668 HelpFormatter - Date/Time: 2013/08/18 11:46:48
[2013-08-18 09:46] INFO 11:46:48,669 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:46] INFO 11:46:48,669 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:46] INFO 11:46:48,676 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
[2013-08-18 09:46] INFO 11:46:49,077 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:46] INFO 11:46:49,143 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2013-08-18 09:46] INFO 11:46:49,149 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:46] INFO 11:46:49,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
[2013-08-18 09:46] INFO 11:46:49,175 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
[2013-08-18 09:46] INFO 11:46:50,729 IntervalUtils - Processing 63564965 bp from intervals
[2013-08-18 09:46] INFO 11:46:52,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:46] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:46] ##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
[2013-08-18 09:46] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
[2013-08-18 09:46] ##### ERROR Please do not post this error to the GATK forum
[2013-08-18 09:46] ##### ERROR
[2013-08-18 09:46] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
[2013-08-18 09:46] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2013-08-18 09:46] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
[2013-08-18 09:46] ##### ERROR
[2013-08-18 09:46] ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
[2013-08-18 09:46] ##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:46] ##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:46] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:46] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 46, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx2500m -Djava.io.tmpdir=/data/proj01/work/tmp/tmpErfC5A -jar /opt/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_FT2/tx/tmpo4r4mz/WES01_WES01_SQ1_FT2.grp -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:46:48,623 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
INFO 11:46:48,665 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:46:48,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
INFO 11:46:48,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:46:48,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:46:48,668 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_FT2/tx/tmpo4r4mz/WES01_WES01_SQ1_FT2.grp -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:46:48,668 HelpFormatter - Date/Time: 2013/08/18 11:46:48
INFO 11:46:48,669 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:46:48,669 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:46:48,676 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
INFO 11:46:49,077 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:46:49,143 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:46:49,149 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:46:49,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:46:49,175 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
INFO 11:46:50,729 IntervalUtils - Processing 63564965 bp from intervals
INFO 11:46:52,120 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
[2013-08-18 09:52] GATK: BaseRecalibrator
[2013-08-18 09:52] INFO 11:52:30,283 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
[2013-08-18 09:52] INFO 11:52:30,331 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:52] INFO 11:52:30,332 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:52] INFO 11:52:30,332 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:52] INFO 11:52:30,332 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:52] INFO 11:52:30,335 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_Mor/tx/tmpx86MJX/WES01_WES01_SQ1_Mor.grp -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --downsample_to_fraction 0.923331697282 --downsampling_type ALL_READS --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2013-08-18 09:52] INFO 11:52:30,335 HelpFormatter - Date/Time: 2013/08/18 11:52:30
[2013-08-18 09:52] INFO 11:52:30,335 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:52] INFO 11:52:30,335 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:52] INFO 11:52:30,343 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
[2013-08-18 09:52] INFO 11:52:30,736 GenomeAnalysisEngine - Strictness is SILENT
[2013-08-18 09:52] INFO 11:52:30,805 GenomeAnalysisEngine - Downsampling Settings: Method: ALL_READS, Target Fraction: 0.92
[2013-08-18 09:52] INFO 11:52:30,812 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2013-08-18 09:52] INFO 11:52:30,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
[2013-08-18 09:52] INFO 11:52:30,843 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
[2013-08-18 09:52] INFO 11:52:32,450 IntervalUtils - Processing 63564965 bp from intervals
[2013-08-18 09:52] INFO 11:52:34,637 GATKRunReport - Uploaded run statistics report to AWS S3
[2013-08-18 09:52] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:52] ##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
[2013-08-18 09:52] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
[2013-08-18 09:52] ##### ERROR Please do not post this error to the GATK forum
[2013-08-18 09:52] ##### ERROR
[2013-08-18 09:52] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
[2013-08-18 09:52] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2013-08-18 09:52] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
[2013-08-18 09:52] ##### ERROR
[2013-08-18 09:52] ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
[2013-08-18 09:52] ##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:52] ##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
[2013-08-18 09:52] ##### ERROR ------------------------------------------------------------------------------------------
[2013-08-18 09:52] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 46, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx2500m -Djava.io.tmpdir=/data/proj01/work/tmp/tmpZphAoT -jar /opt/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_Mor/tx/tmpx86MJX/WES01_WES01_SQ1_Mor.grp -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --downsample_to_fraction 0.923331697282 --downsampling_type ALL_READS --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:52:30,283 ArgumentTypeDescriptor - Dynamically determined type of /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed to be BED
INFO 11:52:30,331 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:52:30,332 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
INFO 11:52:30,332 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:52:30,332 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:52:30,335 HelpFormatter - Program Args: -T BaseRecalibrator -o /data/proj01/work/prealign/WESF120601_B1_Mor/tx/tmpx86MJX/WES01_WES01_SQ1_Mor.grp -I /data/proj01/work/prealign/WESF120601_B1_Mor/WES01_WES01_SQ1_Mor.bam -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa --downsample_to_fraction 0.923331697282 --downsampling_type ALL_READS --knownSites /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf -L /data/proj01/input/SeqCap_EZ_Exome_v3_primary.bed --interval_set_rule INTERSECTION -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
INFO 11:52:30,335 HelpFormatter - Date/Time: 2013/08/18 11:52:30
INFO 11:52:30,335 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:52:30,335 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:52:30,343 ArgumentTypeDescriptor - Dynamically determined type of /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf to be VCF
INFO 11:52:30,736 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:52:30,805 GenomeAnalysisEngine - Downsampling Settings: Method: ALL_READS, Target Fraction: 0.92
INFO 11:52:30,812 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:52:30,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 11:52:30,843 RMDTrackBuilder - Loading Tribble index from disk for file /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation/dbsnp_137.vcf
INFO 11:52:32,450 IntervalUtils - Processing 63564965 bp from intervals
INFO 11:52:34,637 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR knownSites contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
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