manta
manta copied to clipboard
Published
20 hours ago •
Illumina
Illumina
[ERROR] Failed to complete command task
I try to run manta on bam-file (size 11,1 GB) and get a next error:
[2020-08-27T13:58:40.634587Z] [44640fb73383] [344_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/soft/manta-1.6.0/libexec/GetAlignmentStats --ref /var/lib/cwl/stgf2087109-1e88-4817-ad91-7357c962dd8e/ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --output-file /uvvNVB/output/mantaRunDir/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /uvvNVB/output/inputs/260003040807_S14.bam'
[2020-08-27T13:58:40.636291Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 15 stderr lines from task (of 15 total lines):
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.607761Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2020-Aug-27 16:58:40 /soft/manta-1.6.0.release_src/src/c++/lib/manta/ReadGroupStatsUtil.cpp(210): Throw in function void ReadGroupOrientTracker::finalize(const ReadCounter&)
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608170Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException>
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608329Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] std::exception::what: Too few high-confidence read pairs (69) to determine pair orientation for read group '' in bam file '/uvvNVB/output/inputs/260003040807_S14.bam'
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608543Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] At least 100 high-confidence read pairs are required to determine pair orientation.
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608658Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled reads: 622550449
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608760Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled paired reads: 622550449
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608862Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled paired reads passing MAPQ filter: 563645109
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608965Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled high-confidence read pairs passing all filters: 69
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609065Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000]
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609165Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000]
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609265Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000]
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609374Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] cmdline: /soft/manta-1.6.0/libexec/GetAlignmentStats --ref /var/lib/cwl/stgf2087109-1e88-4817-ad91-7357c962dd8e/ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --output-file /uvvNVB/output/mantaRunDir/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /uvvNVB/output/inputs/260003040807_S14.bam
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609478Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] version: 1.6.0
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609581Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] buildTime: 2020-06-15T14:01:44.904013Z
[2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609680Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] compiler: g++-7.5.0
[2020-08-27T13:58:40.639203Z] [44640fb73383] [344_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
It's a part of my file ( sam-file derived from the bam-file):
A01013:110:HCJ3JDSXY:1:2207:19786:3161 2129 chr1 10732 0 120H30M chr7 102930989 0 GCAGGCGCAGAGAGGCGCGCCGCGCCGGCG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr7,102931085,-,125M25S,250,1;
A01013:110:HCJ3JDSXY:2:2141:6497:26960 2145 chr1 16194 0 30M121H chr6 78818173 0 GAGCTGGACCCCTGAGCTAGCCATGCTCTG :F:FFFFF:FFFFFF:FFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr6,78818060,+,25S126M,144,0;
A01013:110:HCJ3JDSXY:3:1608:21540:29841 2113 chr1 19477 0 30M121H = 190561119 190541714 CTCTAAAGGTTGGAATGAATGGCCTAGAAT FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr1,190561316,-,126M25S,250,0;
A01013:110:HCJ3JDSXY:4:1307:1425:12978 2113 chr1 22089 0 30M121H chr16 79884662 0 GTGTGTCATAGTCCCCTGGCCCCATTAATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr16,79885035,-,126M25S,250,0;
A01013:110:HCJ3JDSXY:4:2233:22119:28463 2113 chr1 25704 0 30M121H chr12 105982062 0 CCTATAAATAGGCCTAATCACAGCCCCTCA FFFFFF:FFFFFFFFFFFFFFFFFF::FF, RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr12,105982337,-,8S118M25S,218,5;
A01013:110:HCJ3JDSXY:2:2270:9236:13291 2129 chr1 27785 0 119H30M chr3 106467444 0 ACTGCTAATAATACCTACACATGTTAGAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr3,106467679,-,124M25S,212,5;
A01013:110:HCJ3JDSXY:2:1547:13494:22200 2129 chr1 30776 0 121H30M = 217933355 217902651 CCTTTGGTAGGTAATTACGGTTAGATGAGG FF,FFFFFFFFFFFFFF:,FFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr1,217933407,-,126M25S,110,5;
A01013:110:HCJ3JDSXY:4:1640:26422:3411 2129 chr1 31308 0 121H30M chr2 35378125 0 TCTTTGTGTGACCCTGGGCAAGCCATGAAT FF::FFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr2,35378293,-,126M25S,250,0;
A01013:110:HCJ3JDSXY:4:2146:5177:30906 2129 chr1 33596 0 121H30M chr18 3222972 0 ATGCGTGTGCCATGTTGGTTTGCTGCACCC F,FF:FFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr18,3223230,-,126M25S,198,5;
...
Can you help me with this problem?
我尝试在bam文件（大小为11,1 GB）上运行manta并得到下一个错误：
[2020-08-27T13:58:40.634587Z] [44640fb73383] [344_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/soft/manta-1.6.0/libexec/GetAlignmentStats --ref /var/lib/cwl/stgf2087109-1e88-4817-ad91-7357c962dd8e/ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --output-file /uvvNVB/output/mantaRunDir/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /uvvNVB/output/inputs/260003040807_S14.bam' [2020-08-27T13:58:40.636291Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message: [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 15 stderr lines from task (of 15 total lines): [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.607761Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2020-Aug-27 16:58:40 /soft/manta-1.6.0.release_src/src/c++/lib/manta/ReadGroupStatsUtil.cpp(210): Throw in function void ReadGroupOrientTracker::finalize(const ReadCounter&) [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608170Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException> [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608329Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] std::exception::what: Too few high-confidence read pairs (69) to determine pair orientation for read group '' in bam file '/uvvNVB/output/inputs/260003040807_S14.bam' [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608543Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] At least 100 high-confidence read pairs are required to determine pair orientation. [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608658Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled reads: 622550449 [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608760Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled paired reads: 622550449 [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608862Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled paired reads passing MAPQ filter: 563645109 [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.608965Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] Total sampled high-confidence read pairs passing all filters: 69 [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609065Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609165Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609265Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609374Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] cmdline: /soft/manta-1.6.0/libexec/GetAlignmentStats --ref /var/lib/cwl/stgf2087109-1e88-4817-ad91-7357c962dd8e/ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --output-file /uvvNVB/output/mantaRunDir/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /uvvNVB/output/inputs/260003040807_S14.bam [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609478Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] version: 1.6.0 [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609581Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] buildTime: 2020-06-15T14:01:44.904013Z [2020-08-27T13:58:40.637709Z] [44640fb73383] [344_1] [TaskManager] [ERROR] [2020-08-27T13:58:40.609680Z] [44640fb73383] [344_1] [getAlignmentStats_generateStats_000] compiler: g++-7.5.0 [2020-08-27T13:58:40.639203Z] [44640fb73383] [344_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.这是我文件的一部分（从bam文件派生的sam文件）：
A01013:110:HCJ3JDSXY:1:2207:19786:3161 2129 chr1 10732 0 120H30M chr7 102930989 0 GCAGGCGCAGAGAGGCGCGCCGCGCCGGCG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr7,102931085,-,125M25S,250,1; A01013:110:HCJ3JDSXY:2:2141:6497:26960 2145 chr1 16194 0 30M121H chr6 78818173 0 GAGCTGGACCCCTGAGCTAGCCATGCTCTG :F:FFFFF:FFFFFF:FFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr6,78818060,+,25S126M,144,0; A01013:110:HCJ3JDSXY:3:1608:21540:29841 2113 chr1 19477 0 30M121H = 190561119 190541714 CTCTAAAGGTTGGAATGAATGGCCTAGAAT FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr1,190561316,-,126M25S,250,0; A01013:110:HCJ3JDSXY:4:1307:1425:12978 2113 chr1 22089 0 30M121H chr16 79884662 0 GTGTGTCATAGTCCCCTGGCCCCATTAATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr16,79885035,-,126M25S,250,0; A01013:110:HCJ3JDSXY:4:2233:22119:28463 2113 chr1 25704 0 30M121H chr12 105982062 0 CCTATAAATAGGCCTAATCACAGCCCCTCA FFFFFF:FFFFFFFFFFFFFFFFFF::FF, RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr12,105982337,-,8S118M25S,218,5; A01013:110:HCJ3JDSXY:2:2270:9236:13291 2129 chr1 27785 0 119H30M chr3 106467444 0 ACTGCTAATAATACCTACACATGTTAGAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr3,106467679,-,124M25S,212,5; A01013:110:HCJ3JDSXY:2:1547:13494:22200 2129 chr1 30776 0 121H30M = 217933355 217902651 CCTTTGGTAGGTAATTACGGTTAGATGAGG FF,FFFFFFFFFFFFFF:,FFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr1,217933407,-,126M25S,110,5; A01013:110:HCJ3JDSXY:4:1640:26422:3411 2129 chr1 31308 0 121H30M chr2 35378125 0 TCTTTGTGTGACCCTGGGCAAGCCATGAAT FF::FFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr2,35378293,-,126M25S,250,0; A01013:110:HCJ3JDSXY:4:2146:5177:30906 2129 chr1 33596 0 121H30M chr18 3222972 0 ATGCGTGTGCCATGTTGGTTTGCTGCACCC F,FF:FFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:260003040807_S14 AS:i:30 XS:i:30 NM:i:0 SA:Z:chr18,3223230,-,126M25S,198,5; ...您能帮我解决这个问题吗？
I also encountered the same problem. Have you solved this problem?
