manta SEQ='*' error and how to solve it?

SEQ='*' error and how to solve it?

Open temizna opened this issue 4 years ago • 0 comments

I am trying run manta on whole genomes and I am getting the following errors: Main fatal error boils down to alignment contains SEQ='*' How do I make sure I don't have these alignments? A google search did not show any tools or ways to avoid this. My alignment files do not contain multiple mapped locations. Thanks

more workflow.error.log.txt [2020-04-16T14:30:22.963205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_013_chr13' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_013_chr13 --chrom c hr13' [2020-04-16T14:30:22.963952Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_013_chr13] Error Message: [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_013_chr13] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.880456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.882313Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.883507Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.885371Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.887179Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam_stream_record_no: 13 [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.891735Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:2219:12156:6605/1 [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.902817Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam record RNAME: chr13 [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.907506Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam record POS: 3000016 [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.909089Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.911936Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.916406Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.918133Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_013_chr13 --chrom chr13 [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.923943Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] version: 1.6.0 [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.933425Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.964005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.939227Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] compiler: g++-6.3.1 [2020-04-16T14:30:22.964142Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete. [2020-04-16T14:30:22.976472Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_018_chr18' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_018_chr18 --chrom c hr18' [2020-04-16T14:30:22.976546Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_018_chr18] Error Message: [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_018_chr18] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.880582Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.882526Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.884436Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.886338Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.890945Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam_stream_record_no: 26 [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.893254Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2140:30734:34741/1 [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.894839Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam record RNAME: chr18 [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.896558Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam record POS: 3000001 [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.898290Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.904411Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.905917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.909096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_018_chr18 --chrom chr18 [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.913966Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] version: 1.6.0 [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.918893Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.976593Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.925460Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] compiler: g++-6.3.1 [2020-04-16T14:30:22.976818Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_004_chr4' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_004_chr4 --chrom chr 4' [2020-04-16T14:30:22.976861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_004_chr4] Error Message: [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_004_chr4] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.888087Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.891723Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.901248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.905151Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.909079Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam_stream_record_no: 3 [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.910932Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:1:1415:26711:35759/1 [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.917265Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam record RNAME: chr4 [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.922983Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam record POS: 3050000 [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.924679Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.932522Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.936732Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.937514Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_004_chr4 --chrom chr4 [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.943970Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] version: 1.6.0 [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.944835Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.976901Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.945700Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] compiler: g++-6.3.1 [2020-04-16T14:30:22.978909Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_000_chrM' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chrM --chrom chr M' [2020-04-16T14:30:22.979004Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chrM] Error Message: [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chrM] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.885384Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.887956Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.891704Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.892488Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.894042Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam_stream_record_no: 591 [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.895605Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2319:1226:22686/1 [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.899268Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam record RNAME: chrM [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.902012Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam record POS: 1 [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.903559Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.906684Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.908246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.909064Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chrM --chrom chrM [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.910125Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] version: 1.6.0 [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.914738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.979060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.919684Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] compiler: g++-6.3.1 [2020-04-16T14:30:22.993312Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_007_chr7' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_007_chr7 --chrom chr 7' [2020-04-16T14:30:22.996159Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_007_chr7] Error Message: [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_007_chr7] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.913916Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.919692Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.927041Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.934208Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.935950Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam_stream_record_no: 15 [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.943002Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2317:22272:6558/1 [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.948926Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam record RNAME: chr7 [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.953485Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam record POS: 3000071 [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.954277Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.955849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.961164Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.962692Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_007_chr7 --chrom chr7 [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.965359Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] version: 1.6.0 [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.966937Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.996201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.968473Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] compiler: g++-6.3.1 [2020-04-16T14:30:22.996405Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_014_chr14' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_014_chr14 --chrom c hr14' [2020-04-16T14:30:22.996448Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_014_chr14] Error Message: [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_014_chr14] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.919649Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.927809Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.936739Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.943992Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.948216Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam_stream_record_no: 232 [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.953485Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2228:25120:34945/2 [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.955054Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam record RNAME: chr14 [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.958522Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam record POS: 3001134 [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.966140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.967695Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.969278Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.973626Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_014_chr14 --chrom chr14 [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.975189Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] version: 1.6.0 [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.976021Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.996484Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.976934Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] compiler: g++-6.3.1 [2020-04-16T14:30:22.996661Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_003_chr3' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_003_chr3 --chrom chr 3' [2020-04-16T14:30:22.996704Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_003_chr3] Error Message: [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_003_chr3] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.885502Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.888729Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.890222Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.897543Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.909059Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam_stream_record_no: 64 [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.912958Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:1201:2465:36385/2 [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.919689Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam record RNAME: chr3 [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.926251Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam record POS: 3000000 [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.935076Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.941414Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.948952Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.952726Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_003_chr3 --chrom chr3 [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.954275Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] version: 1.6.0 [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.957541Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:22.996734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.964592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] compiler: g++-6.3.1 [2020-04-16T14:30:23.003867Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_010_chr10' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_010_chr10 --chrom c hr10' [2020-04-16T14:30:23.003919Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_010_chr10] Error Message: [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_010_chr10] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.898095Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.909094Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.915596Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.921526Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.928631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam_stream_record_no: 11 [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.930867Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:1640:8558:6198/2 [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.936732Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam record RNAME: chr10 [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.938302Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam record POS: 3100016 [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.944858Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.946563Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.951889Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.953508Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_010_chr10 --chrom chr10 [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.956742Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] version: 1.6.0 [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.961928Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.003957Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:22.963583Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] compiler: g++-6.3.1 [2020-04-16T14:30:23.075421Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_019_chr19' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_019_chr19 --chrom c hr19' [2020-04-16T14:30:23.075562Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_019_chr19] Error Message: [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_019_chr19] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.025151Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.026101Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.026930Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.027841Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.028651Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam_stream_record_no: 232 [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.031176Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:1606:14181:18317/1 [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.032073Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam record RNAME: chr19 [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.032892Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam record POS: 3079814 [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.033644Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.034427Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.035189Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.035981Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_019_chr19 --chrom chr19 [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.036745Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] version: 1.6.0 [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.037536Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.075616Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.038306Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] compiler: g++-6.3.1 [2020-04-16T14:30:23.088563Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_006_chr6' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_006_chr6 --chrom chr 6' [2020-04-16T14:30:23.088642Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_006_chr6] Error Message: [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_006_chr6] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.057995Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.058947Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.062080Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.062993Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.063953Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam_stream_record_no: 28 [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.064752Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:2232:7934:35650/1 [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.065513Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam record RNAME: chr6 [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.066320Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam record POS: 3050000 [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.067201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.068033Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.068851Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.072268Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_006_chr6 --chrom chr6 [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.073052Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] version: 1.6.0 [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.073878Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.088683Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.074632Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] compiler: g++-6.3.1 [2020-04-16T14:30:23.127228Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_008_chr8' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_008_chr8 --chrom chr 8' [2020-04-16T14:30:23.127311Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_008_chr8] Error Message: [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_008_chr8] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.088456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.089763Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.092183Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.093122Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.093943Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam_stream_record_no: 1397 [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.095012Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2123:29478:27398/1 [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.095964Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam record RNAME: chr8 [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.096877Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam record POS: 3009188 [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.097716Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.098596Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.101169Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.102228Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_008_chr8 --chrom chr8 [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.103140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] version: 1.6.0 [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.103975Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.127381Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.104754Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] compiler: g++-6.3.1 [2020-04-16T14:30:23.136654Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_001_chr1' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_001_chr1 --chrom chr 1' [2020-04-16T14:30:23.136708Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_001_chr1] Error Message: [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_001_chr1] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.106876Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.107706Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.108477Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.109268Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.111737Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam_stream_record_no: 12 [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.112581Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2525:5059:3333/1 [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.113316Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam record RNAME: chr1 [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.114100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam record POS: 3000025 [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.114884Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.115684Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.116580Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.117442Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_001_chr1 --chrom chr1 [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.118191Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] version: 1.6.0 [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.118978Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.136748Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.121639Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] compiler: g++-6.3.1 [2020-04-16T14:30:23.176526Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_005_chr5' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_005_chr5 --chrom chr 5' [2020-04-16T14:30:23.180278Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_005_chr5] Error Message: [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_005_chr5] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.136523Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.137991Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.141839Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.144530Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.145376Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam_stream_record_no: 678 [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.146258Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2521:30192:3834/2 [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.147391Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam record RNAME: chr5 [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.148387Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam record POS: 3001517 [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.152214Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.153924Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.155520Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.156368Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_005_chr5 --chrom chr5 [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.157140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] version: 1.6.0 [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.157938Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.180496Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.158703Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] compiler: g++-6.3.1 [2020-04-16T14:30:23.181300Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_015_chr15' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_015_chr15 --chrom c hr15' [2020-04-16T14:30:23.181353Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_015_chr15] Error Message: [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_015_chr15] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.131482Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.133045Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.133809Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.134728Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.135497Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam_stream_record_no: 458 [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.136313Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:1:2517:9046:21793/1 [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.137087Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam record RNAME: chr15 [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.138801Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam record POS: 3052911 [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.143629Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.144536Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.145382Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.146275Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_015_chr15 --chrom chr15 [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.147395Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] version: 1.6.0 [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.148361Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.181392Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.149237Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] compiler: g++-6.3.1 [2020-04-16T14:30:23.252132Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_011_chr11' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_011_chr11 --chrom c hr11' [2020-04-16T14:30:23.252210Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_011_chr11] Error Message: [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_011_chr11] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.188734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.190760Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.192978Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.194677Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.196455Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam_stream_record_no: 989 [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.198581Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:1109:18403:37027/2 [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.201345Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam record RNAME: chr11 [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.203388Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam record POS: 3100011 [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.206571Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.208435Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.209990Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.212314Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_011_chr11 --chrom chr11 [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.220914Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] version: 1.6.0 [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.224198Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.252248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.229225Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] compiler: g++-6.3.1 [2020-04-16T14:30:23.265507Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_021_chrY' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_021_chrY --chrom chr Y' [2020-04-16T14:30:23.265567Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_021_chrY] Error Message: [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_021_chrY] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.188904Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.192179Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.193834Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.195557Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.197506Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam_stream_record_no: 1284 [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.200059Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:1172:8395:6136/1 [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.202364Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam record RNAME: chrY [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.204213Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam record POS: 134175 [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.205794Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.213948Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.221825Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.225018Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_021_chrY --chrom chrY [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.229246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] version: 1.6.0 [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.233580Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.265609Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.237636Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] compiler: g++-6.3.1 [2020-04-16T14:30:23.268775Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_020_chrX' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_020_chrX --chrom chr X' [2020-04-16T14:30:23.268820Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_020_chrX] Error Message: [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_020_chrX] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.203009Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.204996Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.207544Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.209214Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.211407Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam_stream_record_no: 34 [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.213120Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:1:2348:1298:31955/2 [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.214924Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam record RNAME: chrX [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.222615Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam record POS: 3050120 [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.225737Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.227565Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.232717Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.235271Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_020_chrX --chrom chrX [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.237630Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] version: 1.6.0 [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.240221Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.268849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.245927Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] compiler: g++-6.3.1 [2020-04-16T14:30:23.282305Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_017_chr17' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_017_chr17 --chrom c hr17' [2020-04-16T14:30:23.282570Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_017_chr17] Error Message: [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_017_chr17] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.211841Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.214951Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.223427Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.228451Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.236860Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam_stream_record_no: 29 [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.238591Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:1415:7048:18615/2 [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.243140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam record RNAME: chr17 [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.245143Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam record POS: 3000029 [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.252669Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.253405Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.254968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.255934Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_017_chr17 --chrom chr17 [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.256714Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] version: 1.6.0 [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.258418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.282607Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.262025Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] compiler: g++-6.3.1 [2020-04-16T14:30:23.282786Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_012_chr12' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_012_chr12 --chrom c hr12' [2020-04-16T14:30:23.282826Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_012_chr12] Error Message: [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_012_chr12] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.225419Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.229252Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.234444Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.237637Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.242060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam_stream_record_no: 1475 [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.243136Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2159:11053:3317/2 [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.244060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam record RNAME: chr12 [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.248292Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam record POS: 3003015 [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.252701Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.255951Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.257511Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.259246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_012_chr12 --chrom chr12 [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.262883Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] version: 1.6.0 [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.264537Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.282861Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.266914Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] compiler: g++-6.3.1 [2020-04-16T14:30:23.283025Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_002_chr2' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_002_chr2 --chrom chr 2' [2020-04-16T14:30:23.283064Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr2] Error Message: [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr2] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.215579Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.223415Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.226518Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.231864Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.236070Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam_stream_record_no: 3 [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.237634Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:1659:1714:29731/1 [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.241288Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam record RNAME: chr2 [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.245946Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam record POS: 3050002 [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.246734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.250327Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.255921Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.256715Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_002_chr2 --chrom chr2 [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.258422Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] version: 1.6.0 [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.263664Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.283096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.265321Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] compiler: g++-6.3.1 [2020-04-16T14:30:23.351258Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_016_chr16' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/ RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_016_chr16 --chrom c hr16' [2020-04-16T14:30:23.351382Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_016_chr16] Error Message: [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_016_chr16] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.311807Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SV LocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.313349Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.315273Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.317261Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.318844Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam_stream_record_no: 63 [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.320999Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2611:6831:32612/1 [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.323195Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam record RNAME: chr16 [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.324675Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam record POS: 3016489 [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.326403Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.327937Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.329774Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.331231Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_016_chr16 --chrom chr16 [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.332803Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] version: 1.6.0 [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.334549Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.351418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.336192Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] compiler: g++-6.3.1 [2020-04-16T14:30:23.351591Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_009_chr9' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/R NASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_009_chr9 --chrom chr 9' [2020-04-16T14:30:23.351634Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_009_chr9] Error Message: [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_009_chr9] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.310575Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVL ocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.311536Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.312493Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for variant calling: [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.314348Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.316415Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam_stream_record_no: 36 [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.318070Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2533:9833:4867/1 [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.320159Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam record RNAME: chr9 [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.322130Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam record POS: 2999999 [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.323892Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.325603Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.327169Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.328707Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_009_chr9 --chrom chr9 [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.330476Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] version: 1.6.0 [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.332026Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:23.351668Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [TaskManager] [ERROR] [2020-04-16T14:30:23.333605Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] compiler: g++-6.3.1 [2020-04-16T14:30:39.736096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors: [2020-04-16T14:30:39.736196Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_016_chr16' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_016_chr16 --chro m chr16' [2020-04-16T14:30:39.736246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_016_chr16] Error Message: [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_016_chr16] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.311807Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.313349Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.315273Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.317261Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.318844Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam_stream_record_no: 63 [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.320999Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2611:6831:32612/1 [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.323195Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam record RNAME: chr16 [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.324675Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] bam record POS: 3016489 [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.326403Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.327937Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.329774Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.331231Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_016_chr16 --chrom chr 16 [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.332803Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] version: 1.6.0 [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.334549Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.736282Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.336192Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_016_chr16] compiler: g++-6.3.1 [2020-04-16T14:30:39.736456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_005_chr5' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_005_chr5 --chrom chr5' [2020-04-16T14:30:39.736498Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_005_chr5] Error Message: [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_005_chr5] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.136523Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.137991Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.141839Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.144530Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.145376Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam_stream_record_no: 678 [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.146258Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2521:30192:3834/2 [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.147391Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam record RNAME: chr5 [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.148387Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] bam record POS: 3001517 [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.152214Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.153924Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.155520Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.156368Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_005_chr5 --chrom chr5 [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.157140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] version: 1.6.0 [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.157938Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.736532Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.158703Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_005_chr5] compiler: g++-6.3.1 [2020-04-16T14:30:39.736638Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_006_chr6' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_006_chr6 --chrom chr6' [2020-04-16T14:30:39.736679Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_006_chr6] Error Message: [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_006_chr6] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.057995Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.058947Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.062080Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.062993Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.063953Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam_stream_record_no: 28 [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.064752Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:2232:7934:35650/1 [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.065513Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam record RNAME: chr6 [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.066320Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] bam record POS: 3050000 [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.067201Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.068033Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.068851Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.072268Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_006_chr6 --chrom chr6 [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.073052Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] version: 1.6.0 [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.073878Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.736712Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.074632Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_006_chr6] compiler: g++-6.3.1 [2020-04-16T14:30:39.739847Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_008_chr8' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_008_chr8 --chrom chr8' [2020-04-16T14:30:39.739903Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_008_chr8] Error Message: [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_008_chr8] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.088456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.089763Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.092183Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.093122Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.093943Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam_stream_record_no: 1397 [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.095012Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2123:29478:27398/1 [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.095964Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam record RNAME: chr8 [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.096877Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] bam record POS: 3009188 [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.097716Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.098596Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.101169Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.102228Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_008_chr8 --chrom chr8 [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.103140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] version: 1.6.0 [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.103975Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.739940Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.104754Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_008_chr8] compiler: g++-6.3.1 [2020-04-16T14:30:39.740047Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_003_chr3' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_003_chr3 --chrom chr3' [2020-04-16T14:30:39.740085Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_003_chr3] Error Message: [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_003_chr3] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.885502Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.888729Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.890222Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.897543Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.909059Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam_stream_record_no: 64 [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.912958Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:1201:2465:36385/2 [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.919689Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam record RNAME: chr3 [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.926251Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] bam record POS: 3000000 [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.935076Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.941414Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.948952Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.952726Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_003_chr3 --chrom chr3 [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.954275Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] version: 1.6.0 [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.957541Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.740117Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.964592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_003_chr3] compiler: g++-6.3.1 [2020-04-16T14:30:39.740221Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_017_chr17' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_017_chr17 --chro m chr17' [2020-04-16T14:30:39.740262Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_017_chr17] Error Message: [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_017_chr17] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.211841Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.214951Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.223427Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.228451Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.236860Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam_stream_record_no: 29 [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.238591Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:1415:7048:18615/2 [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.243140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam record RNAME: chr17 [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.245143Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] bam record POS: 3000029 [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.252669Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.253405Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.254968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.255934Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_017_chr17 --chrom chr 17 [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.256714Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] version: 1.6.0 [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.258418Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.740294Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.262025Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_017_chr17] compiler: g++-6.3.1 [2020-04-16T14:30:39.743650Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_021_chrY' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_021_chrY --chrom chrY' [2020-04-16T14:30:39.743702Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_021_chrY] Error Message: [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_021_chrY] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.188904Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.192179Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.193834Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.195557Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.197506Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam_stream_record_no: 1284 [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.200059Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:1172:8395:6136/1 [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.202364Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam record RNAME: chrY [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.204213Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] bam record POS: 134175 [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.205794Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.213948Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.221825Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.225018Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_021_chrY --chrom chrY [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.229246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] version: 1.6.0 [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.233580Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.743738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.237636Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_021_chrY] compiler: g++-6.3.1 [2020-04-16T14:30:39.743844Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_014_chr14' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_014_chr14 --chro m chr14' [2020-04-16T14:30:39.743881Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_014_chr14] Error Message: [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_014_chr14] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.919649Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.927809Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.936739Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.943992Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.948216Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam_stream_record_no: 232 [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.953485Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2228:25120:34945/2 [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.955054Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam record RNAME: chr14 [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.958522Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] bam record POS: 3001134 [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.966140Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.967695Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.969278Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.973626Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_014_chr14 --chrom chr 14 [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.975189Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] version: 1.6.0 [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.976021Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.743917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.976934Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_014_chr14] compiler: g++-6.3.1 [2020-04-16T14:30:39.744026Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_011_chr11' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_011_chr11 --chro m chr11' [2020-04-16T14:30:39.744067Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_011_chr11] Error Message: [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_011_chr11] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.188734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.190760Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.192978Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.194677Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.196455Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam_stream_record_no: 989 [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.198581Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:1109:18403:37027/2 [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.201345Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam record RNAME: chr11 [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.203388Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] bam record POS: 3100011 [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.206571Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.208435Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.209990Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.212314Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_011_chr11 --chrom chr 11 [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.220914Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] version: 1.6.0 [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.224198Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.744100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.229225Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_011_chr11] compiler: g++-6.3.1 [2020-04-16T14:30:39.744203Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_007_chr7' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_007_chr7 --chrom chr7' [2020-04-16T14:30:39.744239Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_007_chr7] Error Message: [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_007_chr7] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.913916Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.919692Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.927041Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.934208Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.935950Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam_stream_record_no: 15 [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.943002Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2317:22272:6558/1 [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.948926Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam record RNAME: chr7 [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.953485Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] bam record POS: 3000071 [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.954277Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.955849Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.961164Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.962692Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_007_chr7 --chrom chr7 [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.965359Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] version: 1.6.0 [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.966937Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.744272Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.968473Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_007_chr7] compiler: g++-6.3.1 [2020-04-16T14:30:39.744387Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_018_chr18' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_018_chr18 --chro m chr18' [2020-04-16T14:30:39.744425Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_018_chr18] Error Message: [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_018_chr18] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.880582Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.882526Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.884436Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.886338Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.890945Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam_stream_record_no: 26 [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.893254Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2140:30734:34741/1 [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.894839Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam record RNAME: chr18 [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.896558Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] bam record POS: 3000001 [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.898290Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.904411Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.905917Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.909096Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_018_chr18 --chrom chr 18 [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.913966Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] version: 1.6.0 [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.918893Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.744456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.925460Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_018_chr18] compiler: g++-6.3.1 [2020-04-16T14:30:39.744558Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_004_chr4' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_004_chr4 --chrom chr4' [2020-04-16T14:30:39.744598Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_004_chr4] Error Message: [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_004_chr4] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.888087Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.891723Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.901248Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.905151Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.909079Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam_stream_record_no: 3 [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.910932Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:1:1415:26711:35759/1 [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.917265Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam record RNAME: chr4 [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.922983Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] bam record POS: 3050000 [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.924679Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.932522Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.936732Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.937514Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_004_chr4 --chrom chr4 [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.943970Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] version: 1.6.0 [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.944835Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.744631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.945700Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_004_chr4] compiler: g++-6.3.1 [2020-04-16T14:30:39.744735Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_015_chr15' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_015_chr15 --chro m chr15' [2020-04-16T14:30:39.744770Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_015_chr15] Error Message: [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_015_chr15] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.131482Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.133045Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.133809Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.134728Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.135497Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam_stream_record_no: 458 [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.136313Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:1:2517:9046:21793/1 [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.137087Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam record RNAME: chr15 [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.138801Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] bam record POS: 3052911 [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.143629Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.144536Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.145382Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.146275Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_015_chr15 --chrom chr 15 [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.147395Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] version: 1.6.0 [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.148361Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.744802Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.149237Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_015_chr15] compiler: g++-6.3.1 [2020-04-16T14:30:39.744903Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_010_chr10' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_010_chr10 --chro m chr10' [2020-04-16T14:30:39.744937Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_010_chr10] Error Message: [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_010_chr10] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.898095Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.909094Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.915596Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.921526Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.928631Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam_stream_record_no: 11 [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.930867Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:1640:8558:6198/2 [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.936732Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam record RNAME: chr10 [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.938302Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] bam record POS: 3100016 [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.944858Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.946563Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.951889Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.953508Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_010_chr10 --chrom chr 10 [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.956742Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] version: 1.6.0 [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.961928Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.744968Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.963583Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_010_chr10] compiler: g++-6.3.1 [2020-04-16T14:30:39.745067Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_013_chr13' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_013_chr13 --chro m chr13' [2020-04-16T14:30:39.745106Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_013_chr13] Error Message: [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_013_chr13] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.880456Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.882313Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.883507Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.885371Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.887179Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam_stream_record_no: 13 [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.891735Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:2219:12156:6605/1 [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.902817Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam record RNAME: chr13 [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.907506Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] bam record POS: 3000016 [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.909089Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.911936Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.916406Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.918133Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_013_chr13 --chrom chr 13 [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.923943Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] version: 1.6.0 [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.933425Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.745139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.939227Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_013_chr13] compiler: g++-6.3.1 [2020-04-16T14:30:39.748080Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_019_chr19' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_019_chr19 --chro m chr19' [2020-04-16T14:30:39.748139Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_019_chr19] Error Message: [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_019_chr19] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.025151Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.026101Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.026930Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.027841Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.028651Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam_stream_record_no: 232 [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.031176Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:1606:14181:18317/1 [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.032073Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam record RNAME: chr19 [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.032892Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] bam record POS: 3079814 [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.033644Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.034427Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.035189Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.035981Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_019_chr19 --chrom chr 19 [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.036745Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] version: 1.6.0 [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.037536Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.748180Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.038306Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_019_chr19] compiler: g++-6.3.1 [2020-04-16T14:30:39.748287Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_002_chr2' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_002_chr2 --chrom chr2' [2020-04-16T14:30:39.748324Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr2] Error Message: [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr2] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.215579Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.223415Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.226518Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.231864Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.236070Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam_stream_record_no: 3 [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.237634Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:4:1659:1714:29731/1 [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.241288Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam record RNAME: chr2 [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.245946Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] bam record POS: 3050002 [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.246734Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.250327Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.255921Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.256715Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_002_chr2 --chrom chr2 [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.258422Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] version: 1.6.0 [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.263664Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.748592Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.265321Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_002_chr2] compiler: g++-6.3.1 [2020-04-16T14:30:39.748703Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_012_chr12' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shar ed/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_012_chr12 --chro m chr12' [2020-04-16T14:30:39.748744Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_012_chr12] Error Message: [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_012_chr12] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.225419Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.229252Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.234444Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for vari ant calling: [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.237637Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.242060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam_stream_record_no: 1475 [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.243136Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2159:11053:3317/2 [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.244060Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam record RNAME: chr12 [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.248292Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] bam record POS: 3003015 [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.252701Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.255951Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.257511Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.259246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RN ASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_012_chr12 --chrom chr 12 [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.262883Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] version: 1.6.0 [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.264537Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.748781Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.266914Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_012_chr12] compiler: g++-6.3.1 [2020-04-16T14:30:39.751936Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_000_chrM' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chrM --chrom chrM' [2020-04-16T14:30:39.751988Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chrM] Error Message: [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chrM] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.885384Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] FATAL_ERROR: 2020-Apr-16 09:30:22 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.887956Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.891704Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.892488Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.894042Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam_stream_record_no: 591 [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.895605Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2319:1226:22686/1 [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.899268Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam record RNAME: chrM [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.902012Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] bam record POS: 1 [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.903559Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.906684Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.908246Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.909064Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chrM --chrom chrM [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.910125Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] version: 1.6.0 [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.914738Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.752028Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:22.919684Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_000_chrM] compiler: g++-6.3.1 [2020-04-16T14:30:39.752136Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_020_chrX' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_020_chrX --chrom chrX' [2020-04-16T14:30:39.752173Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_020_chrX] Error Message: [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_020_chrX] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.203009Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.204996Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.207544Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.209214Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.211407Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam_stream_record_no: 34 [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.213120Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:1:2348:1298:31955/2 [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.214924Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam record RNAME: chrX [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.222615Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] bam record POS: 3050120 [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.225737Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.227565Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.232717Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.235271Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_020_chrX --chrom chrX [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.237630Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] version: 1.6.0 [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.240221Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.752205Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.245927Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_020_chrX] compiler: g++-6.3.1 [2020-04-16T14:30:39.752310Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_001_chr1' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_001_chr1 --chrom chr1' [2020-04-16T14:30:39.752783Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_001_chr1] Error Message: [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_001_chr1] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.106876Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.107706Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.108477Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.109268Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.111737Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam_stream_record_no: 12 [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.112581Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:3:2525:5059:3333/1 [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.113316Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam record RNAME: chr1 [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.114100Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] bam record POS: 3000025 [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.114884Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.115684Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.116580Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.117442Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_001_chr1 --chrom chr1 [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.118191Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] version: 1.6.0 [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.118978Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.752828Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.121639Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_001_chr1] compiler: g++-6.3.1 [2020-04-16T14:30:39.752936Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_009_chr9' launched from master workflow, error code: 1, command: '/home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/share d/RNASEQ/index/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_009_chr9 --chrom chr9' [2020-04-16T14:30:39.752972Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_009_chr9] Error Message: [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_009_chr9] Last 15 stderr lines from task (of 15 total lines): [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.310575Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] FATAL_ERROR: 2020-Apr-16 09:30:23 /builder/src/c++/lib/manta/SVLocusScanner.cpp(1344): Throw in function static void SVLocusScanner::checkReadSize(const stream_state_reporter&, const bam_record&) [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.311536Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.312493Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] std::exception::what: Input alignment record contains unknown read sequence (SEQ=''), which cannot be used for varia nt calling: [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.314348Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam_stream_label: '/home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam' [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.316415Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam_stream_record_no: 36 [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.318070Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam_record QNAME/read_number: A00223:235:HJGMVDSXX:2:2533:9833:4867/1 [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.320159Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam record RNAME: chr9 [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.322130Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] bam record POS: 2999999 [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.323892Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.325603Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.327169Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.328707Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] cmdline: /home/harrisr/temizna/manta-1.6.0.centos6_x86_64/libexec/GetChromDepth --ref /home/harrisr/shared/RNASEQ/ind ex/Mus_musculus/mm10_canonical/bwa/mm10_canonical.fa --align-file /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_normal.merged.uniq.bam --output /home/harrisr/shared/A3A_APC/speedSomatic/A3A_APC_23_somatic_manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_009_chr9 --chrom chr9 [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.330476Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] version: 1.6.0 [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.332026Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] buildTime: 2019-06-28T22:06:27.673004Z [2020-04-16T14:30:39.753005Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [WorkflowRunner] [ERROR] [2020-04-16T14:30:23.333605Z] [cn0014.mesabi.msi.umn.edu] [21131_1] [getChromDepth_sample000_estimateChromDepth_009_chr9] compiler: g++-6.3.1

Apr 16 '20 15:04 temizna

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SEQ='*' error and how to solve it?

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