search

Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
404 stars 154 forks source link

error workflow generate #164

Closed huangl07 closed 5 years ago

huangl07 commented 5 years ago

[2018-12-13T00:22:16.631416Z] [s25608.local] [13881_1] [TaskManager] [ERROR] Failed to complete command task: 'generateCandidateSV_0001' launched from master workflow, error code: 1, command: '/mnt/ilustre/centos7users/dna/.env/manta-1.4.0.centos6_x86_64/libexec/GenerateSVCandidates --align-stats /mnt/ilustre/centos7users/dna/canvas/workspace/alignmentStats.xml --graph-file /mnt/ilustre/centos7users/dna/canvas/workspace/svLocusGraph.bin --bin-index 1 --bin-count 256 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180801043_zhangjianwei_insert/var_CHO_plasmid1_20180907/02.ref-config/ref.fa --candidate-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/candidateSV.0001.vcf --diploid-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/diploidSV.0001.vcf --min-qual-score 10 --min-pass-qual-score 20 --min-pass-gt-score 15 --enable-remote-read-retrieval --chrom-depth /mnt/ilustre/centos7users/dna/canvas/workspace/chromDepth.txt --edge-runtime-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeRuntimeLog.0001.txt --edge-stats-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeStats.0001.xml --align-file /mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam' [2018-12-13T00:22:16.652530Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [generateCandidateSV_0001] Error Message: [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [generateCandidateSV_0001] Last 32 stderr lines from task (of 32 total lines): [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.208119Z] [s25608.local] [13881_1] [generateCandidateSV_0001] FATAL_ERROR: 2018-Dec-13 08:22:16 /builder/src/c++/lib/applications/GenerateSVCandidates/SVScorePairAltProcessor.cpp(208): Throw in function bool SVScorePairAltProcessor::realignPairedRead(const bam_header_info&, const string&, bool, const string&, int, pos_t, int&) [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.215552Z] [s25608.local] [13881_1] [generateCandidateSV_0001] Dynamic exception type: boost::exception_detail::clone_impl [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.222624Z] [s25608.local] [13881_1] [generateCandidateSV_0001] std::exception::what: Empty read attributed to sequence fragment with QNAME: 'A00283:46:H5NVJDSXX:2:2550:12355:15906' anchored by mate alignment starting at (1-indexed) position: 'sca21:1567183' [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.229843Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [runGSC(GSCOptions const&, char const, char const)::current_edge_info] = Exception caught while processing graph edge: edgeinfo locus:node1:node2: 10:612:612 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.236341Z] [s25608.local] [13881_1] [generateCandidateSV_0001] node1:LocusNode: GenomeInterval: 20:[1567166,1568322) n_edges: 7 out_count: 174 evidence: [1567015,1568003) [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.243339Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 601 out_count: 12 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.250401Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 605 out_count: 18 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.257300Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 612 out_count: 24 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.264378Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 613 out_count: 84 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.271347Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 614 out_count: 18 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.278411Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 615 out_count: 9 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.282414Z] [s25608.local] [13881_1] [generateCandidateSV_0001] EdgeTo: 616 out_count: 9 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.289323Z] [s25608.local] [13881_1] [generateCandidateSV_0001] node1:EndUserGenomeInterval: sca21:1567167-1568322 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.296396Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.303373Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [SVScorer::scoreSV(SVCandidateSetData const&, std::vector<SVCandidateAssemblyData, std::allocator > const&, SVMultiJunctionCandidate const&, std::vector<SVId, std::allocator > const&, std::vector<bool, std::allocator > const&, bool, bool, std::vector<SVModelScoreInfo, std::allocator >&, SVModelScoreInfo&, bool&, SupportSamples&)::scoring_candidate_info] = Exception caught while attempting to score SVCandidate: [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.310491Z] [s25608.local] [13881_1] [generateCandidateSV_0001] isImprecise?: 0 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.317337Z] [s25608.local] [13881_1] [generateCandidateSV_0001] forwardTranscriptStrandReadCount: 0 ; reverseTranscriptStrandReadCount: 0 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.324462Z] [s25608.local] [13881_1] [generateCandidateSV_0001] index candidate:assemblyAlign:assemblySegment: 0:0:0 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.331546Z] [s25608.local] [13881_1] [generateCandidateSV_0001] Alignment: 104I [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.338499Z] [s25608.local] [13881_1] [generateCandidateSV_0001] BreakendInsertSeq: GAGAATTAAATAGGTTCATTTGTAATAACTTCGAAAATAAGTAAGTGAACGGGCTGGAATGAAATCTCAGAGGTTAAGAACACTTGTTTCTCTTACAGAGGAGG [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.345421Z] [s25608.local] [13881_1] [generateCandidateSV_0001] Breakend: GenomeInterval: 20:[1567434,1567435) RIGHT_OPEN [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.351403Z] [s25608.local] [13881_1] [generateCandidateSV_0001] SVBreakendLowResEvidence: pair: 0 local_pair: 0 cigar: 0 softclip: 0 semialign: 4 shadow: 0 split_align: 0 unknown: 0 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.358465Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.365358Z] [s25608.local] [13881_1] [generateCandidateSV_0001] Breakend: GenomeInterval: 20:[1567435,1567436) LEFT_OPEN [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.372388Z] [s25608.local] [13881_1] [generateCandidateSV_0001] SVBreakendLowResEvidence: pair: 0 local_pair: 0 cigar: 0 softclip: 0 semialign: 0 shadow: 0 split_align: 0 unknown: 0 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.377670Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.387215Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.394412Z] [s25608.local] [13881_1] [generateCandidateSV_0001] [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.401249Z] [s25608.local] [13881_1] [generateCandidateSV_0001] cmdline: /mnt/ilustre/centos7users/dna/.env/manta-1.4.0.centos6_x86_64/libexec/GenerateSVCandidates --align-stats /mnt/ilustre/centos7users/dna/canvas/workspace/alignmentStats.xml --graph-file /mnt/ilustre/centos7users/dna/canvas/workspace/svLocusGraph.bin --bin-index 1 --bin-count 256 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180801043_zhangjianwei_insert/var_CHO_plasmid1_20180907/02.ref-config/ref.fa --candidate-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/candidateSV.0001.vcf --diploid-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/diploidSV.0001.vcf --min-qual-score 10 --min-pass-qual-score 20 --min-pass-gt-score 15 --enable-remote-read-retrieval --chrom-depth /mnt/ilustre/centos7users/dna/canvas/workspace/chromDepth.txt --edge-runtime-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeRuntimeLog.0001.txt --edge-stats-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeStats.0001.xml --align-file /mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.408354Z] [s25608.local] [13881_1] [generateCandidateSV_0001] version: 1.4.0 [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.415255Z] [s25608.local] [13881_1] [generateCandidateSV_0001] buildTime: 2018-04-26T23:54:06.820784Z [2018-12-13T00:22:16.672406Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:22:16.422322Z] [s25608.local] [13881_1] [generateCandidateSV_0001] compiler: g++-6.3.1 [2018-12-13T00:22:16.687471Z] [s25608.local] [13881_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete. [2018-12-13T00:24:40.875096Z] [s25608.local] [13881_1] [TaskManager] [ERROR] Failed to complete command task: 'generateCandidateSV_0003' launched from master workflow, error code: 1, command: '/mnt/ilustre/centos7users/dna/.env/manta-1.4.0.centos6_x86_64/libexec/GenerateSVCandidates --align-stats /mnt/ilustre/centos7users/dna/canvas/workspace/alignmentStats.xml --graph-file /mnt/ilustre/centos7users/dna/canvas/workspace/svLocusGraph.bin --bin-index 3 --bin-count 256 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180801043_zhangjianwei_insert/var_CHO_plasmid1_20180907/02.ref-config/ref.fa --candidate-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/candidateSV.0003.vcf --diploid-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/diploidSV.0003.vcf --min-qual-score 10 --min-pass-qual-score 20 --min-pass-gt-score 15 --enable-remote-read-retrieval --chrom-depth /mnt/ilustre/centos7users/dna/canvas/workspace/chromDepth.txt --edge-runtime-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeRuntimeLog.0003.txt --edge-stats-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeStats.0003.xml --align-file /mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam' [2018-12-13T00:24:40.898683Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [generateCandidateSV_0003] Error Message: [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [generateCandidateSV_0003] Last 29 stderr lines from task (of 29 total lines): [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.594077Z] [s25608.local] [13881_1] [generateCandidateSV_0003] FATAL_ERROR: 2018-Dec-13 08:24:40 /builder/src/c++/lib/applications/GenerateSVCandidates/SVScorePairAltProcessor.cpp(208): Throw in function bool SVScorePairAltProcessor::realignPairedRead(const bam_header_info&, const string&, bool, const string&, int, pos_t, int&) [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.602172Z] [s25608.local] [13881_1] [generateCandidateSV_0003] Dynamic exception type: boost::exception_detail::clone_impl [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.609616Z] [s25608.local] [13881_1] [generateCandidateSV_0003] std::exception::what: Empty read attributed to sequence fragment with QNAME: 'A00283:46:H5NVJDSXX:2:1509:32081:32158' anchored by mate alignment starting at (1-indexed) position: 'sca25:2361511' [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.616678Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [runGSC(GSCOptions const&, char const, char const)::current_edge_info] = Exception caught while processing graph edge: edgeinfo locus:node1:node2: 10:988:988 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.623682Z] [s25608.local] [13881_1] [generateCandidateSV_0003] node1:LocusNode: GenomeInterval: 24:[2361360,2361961) n_edges: 4 out_count: 60 evidence: [2361209,2362096) [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.630707Z] [s25608.local] [13881_1] [generateCandidateSV_0003] EdgeTo: 192 out_count: 9 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.637579Z] [s25608.local] [13881_1] [generateCandidateSV_0003] EdgeTo: 988 out_count: 15 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.645098Z] [s25608.local] [13881_1] [generateCandidateSV_0003] EdgeTo: 989 out_count: 12 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.651645Z] [s25608.local] [13881_1] [generateCandidateSV_0003] EdgeTo: 990 out_count: 24 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.658589Z] [s25608.local] [13881_1] [generateCandidateSV_0003] node1:EndUserGenomeInterval: sca25:2361361-2361961 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.666337Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.673642Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [SVScorer::scoreSV(SVCandidateSetData const&, std::vector<SVCandidateAssemblyData, std::allocator > const&, SVMultiJunctionCandidate const&, std::vector<SVId, std::allocator > const&, std::vector<bool, std::allocator > const&, bool, bool, std::vector<SVModelScoreInfo, std::allocator >&, SVModelScoreInfo&, bool&, SupportSamples&)::scoring_candidate_info] = Exception caught while attempting to score SVCandidate: [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.680682Z] [s25608.local] [13881_1] [generateCandidateSV_0003] isImprecise?: 0 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.687625Z] [s25608.local] [13881_1] [generateCandidateSV_0003] forwardTranscriptStrandReadCount: 0 ; reverseTranscriptStrandReadCount: 0 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.694614Z] [s25608.local] [13881_1] [generateCandidateSV_0003] index candidate:assemblyAlign:assemblySegment: 0:0:0 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.701615Z] [s25608.local] [13881_1] [generateCandidateSV_0003] Alignment: 187I29D [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.708621Z] [s25608.local] [13881_1] [generateCandidateSV_0003] BreakendInsertSeq: AGACCTGCTCCCCCCTTCCCCCCCCACCCCCCCACCCCCCTGGCATCCTGCAAGCTCTTACATATCTTAGGCTTTGGAAAATTGAGCCAAATAATATTTTTAACTCTTCCCAGTCTCTCCCTCTCTCCTCTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCATCTCAG [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.715568Z] [s25608.local] [13881_1] [generateCandidateSV_0003] Breakend: GenomeInterval: 24:[2361692,2361693) RIGHT_OPEN [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.722737Z] [s25608.local] [13881_1] [generateCandidateSV_0003] SVBreakendLowResEvidence: pair: 0 local_pair: 0 cigar: 0 softclip: 0 semialign: 5 shadow: 0 split_align: 0 unknown: 0 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.729568Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.734218Z] [s25608.local] [13881_1] [generateCandidateSV_0003] Breakend: GenomeInterval: 24:[2361722,2361723) LEFT_OPEN [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.741666Z] [s25608.local] [13881_1] [generateCandidateSV_0003] SVBreakendLowResEvidence: pair: 0 local_pair: 0 cigar: 0 softclip: 0 semialign: 0 shadow: 0 split_align: 0 unknown: 0 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.745753Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.752575Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.759560Z] [s25608.local] [13881_1] [generateCandidateSV_0003] [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.766763Z] [s25608.local] [13881_1] [generateCandidateSV_0003] cmdline: /mnt/ilustre/centos7users/dna/.env/manta-1.4.0.centos6_x86_64/libexec/GenerateSVCandidates --align-stats /mnt/ilustre/centos7users/dna/canvas/workspace/alignmentStats.xml --graph-file /mnt/ilustre/centos7users/dna/canvas/workspace/svLocusGraph.bin --bin-index 3 --bin-count 256 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180801043_zhangjianwei_insert/var_CHO_plasmid1_20180907/02.ref-config/ref.fa --candidate-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/candidateSV.0003.vcf --diploid-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/diploidSV.0003.vcf --min-qual-score 10 --min-pass-qual-score 20 --min-pass-gt-score 15 --enable-remote-read-retrieval --chrom-depth /mnt/ilustre/centos7users/dna/canvas/workspace/chromDepth.txt --edge-runtime-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeRuntimeLog.0003.txt --edge-stats-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeStats.0003.xml --align-file /mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.773588Z] [s25608.local] [13881_1] [generateCandidateSV_0003] version: 1.4.0 [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.780527Z] [s25608.local] [13881_1] [generateCandidateSV_0003] buildTime: 2018-04-26T23:54:06.820784Z [2018-12-13T00:24:40.921524Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:40.787615Z] [s25608.local] [13881_1] [generateCandidateSV_0003] compiler: g++-6.3.1 [2018-12-13T00:24:43.614934Z] [s25608.local] [13881_1] [TaskManager] [ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1, command: '/mnt/ilustre/centos7users/dna/.env/manta-1.4.0.centos6_x86_64/libexec/GenerateSVCandidates --align-stats /mnt/ilustre/centos7users/dna/canvas/workspace/alignmentStats.xml --graph-file /mnt/ilustre/centos7users/dna/canvas/workspace/svLocusGraph.bin --bin-index 0 --bin-count 256 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180801043_zhangjianwei_insert/var_CHO_plasmid1_20180907/02.ref-config/ref.fa --candidate-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/diploidSV.0000.vcf --min-qual-score 10 --min-pass-qual-score 20 --min-pass-gt-score 15 --enable-remote-read-retrieval --chrom-depth /mnt/ilustre/centos7users/dna/canvas/workspace/chromDepth.txt --edge-runtime-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeStats.0000.xml --align-file /mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam' [2018-12-13T00:24:44.150890Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Error Message: [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Last 30 stderr lines from task (of 30 total lines): [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.308086Z] [s25608.local] [13881_1] [generateCandidateSV_0000] FATAL_ERROR: 2018-Dec-13 08:24:43 /builder/src/c++/lib/applications/GenerateSVCandidates/SVScorePairAltProcessor.cpp(208): Throw in function bool SVScorePairAltProcessor::realignPairedRead(const bam_header_info&, const string&, bool, const string&, int, pos_t, int&) [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.317255Z] [s25608.local] [13881_1] [generateCandidateSV_0000] Dynamic exception type: boost::exception_detail::clone_impl [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.322295Z] [s25608.local] [13881_1] [generateCandidateSV_0000] std::exception::what: Empty read attributed to sequence fragment with QNAME: 'A00283:46:H5NVJDSXX:2:1615:22055:10661' anchored by mate alignment starting at (1-indexed) position: 'sca1941:28642' [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.329694Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [runGSC(GSCOptions const&, char const, char const)::current_edge_info] = Exception caught while processing graph edge: edgeinfo locus:node1:node2: 10:71:71 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.336847Z] [s25608.local] [13881_1] [generateCandidateSV_0000] node1:LocusNode: GenomeInterval: 1940:[28355,29124) n_edges: 5 out_count: 54 evidence: [28204,29188) [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.343718Z] [s25608.local] [13881_1] [generateCandidateSV_0000] EdgeTo: 70 out_count: 0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.350602Z] [s25608.local] [13881_1] [generateCandidateSV_0000] EdgeTo: 71 out_count: 21 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.357624Z] [s25608.local] [13881_1] [generateCandidateSV_0000] EdgeTo: 13482 out_count: 9 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.364560Z] [s25608.local] [13881_1] [generateCandidateSV_0000] EdgeTo: 36991 out_count: 12 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.371648Z] [s25608.local] [13881_1] [generateCandidateSV_0000] EdgeTo: 51563 out_count: 12 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.378639Z] [s25608.local] [13881_1] [generateCandidateSV_0000] node1:EndUserGenomeInterval: sca1941:28356-29124 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.385785Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.392647Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [SVScorer::scoreSV(SVCandidateSetData const&, std::vector<SVCandidateAssemblyData, std::allocator > const&, SVMultiJunctionCandidate const&, std::vector<SVId, std::allocator > const&, std::vector<bool, std::allocator > const&, bool, bool, std::vector<SVModelScoreInfo, std::allocator >&, SVModelScoreInfo&, bool&, SupportSamples&)::scoring_candidate_info] = Exception caught while attempting to score SVCandidate: [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.396925Z] [s25608.local] [13881_1] [generateCandidateSV_0000] isImprecise?: 0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.425303Z] [s25608.local] [13881_1] [generateCandidateSV_0000] forwardTranscriptStrandReadCount: 0 ; reverseTranscriptStrandReadCount: 0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.432767Z] [s25608.local] [13881_1] [generateCandidateSV_0000] index candidate:assemblyAlign:assemblySegment: 0:0:0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.439500Z] [s25608.local] [13881_1] [generateCandidateSV_0000] Alignment: 120I [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.447071Z] [s25608.local] [13881_1] [generateCandidateSV_0000] BreakendInsertSeq: GGGTGGATGGGGTGGGGGGTAGGTTGGGGGTAGGGGAGGAGGGATGGGGGTGAGGGGAGGGAGAGGGAGAAGGGACTTACATGTGAAACAAGCTTGTTCCCTAACTAGAACTAATAATAA [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.453639Z] [s25608.local] [13881_1] [generateCandidateSV_0000] Breakend: GenomeInterval: 1940:[28867,28868) RIGHT_OPEN [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.460754Z] [s25608.local] [13881_1] [generateCandidateSV_0000] SVBreakendLowResEvidence: pair: 0 local_pair: 0 cigar: 0 softclip: 0 semialign: 7 shadow: 0 split_align: 0 unknown: 0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.467772Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.474959Z] [s25608.local] [13881_1] [generateCandidateSV_0000] Breakend: GenomeInterval: 1940:[28868,28869) LEFT_OPEN [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.481644Z] [s25608.local] [13881_1] [generateCandidateSV_0000] SVBreakendLowResEvidence: pair: 0 local_pair: 0 cigar: 0 softclip: 0 semialign: 0 shadow: 0 split_align: 0 unknown: 0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.486047Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.492452Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.499484Z] [s25608.local] [13881_1] [generateCandidateSV_0000] [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.506494Z] [s25608.local] [13881_1] [generateCandidateSV_0000] cmdline: /mnt/ilustre/centos7users/dna/.env/manta-1.4.0.centos6_x86_64/libexec/GenerateSVCandidates --align-stats /mnt/ilustre/centos7users/dna/canvas/workspace/alignmentStats.xml --graph-file /mnt/ilustre/centos7users/dna/canvas/workspace/svLocusGraph.bin --bin-index 0 --bin-count 256 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180801043_zhangjianwei_insert/var_CHO_plasmid1_20180907/02.ref-config/ref.fa --candidate-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/diploidSV.0000.vcf --min-qual-score 10 --min-pass-qual-score 20 --min-pass-gt-score 15 --enable-remote-read-retrieval --chrom-depth /mnt/ilustre/centos7users/dna/canvas/workspace/chromDepth.txt --edge-runtime-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /mnt/ilustre/centos7users/dna/canvas/workspace/svHyGen/edgeStats.0000.xml --align-file /mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.513518Z] [s25608.local] [13881_1] [generateCandidateSV_0000] version: 1.4.0 [2018-12-13T00:24:44.189785Z] [s25608.local] [13881_1] [TaskManager] [ERROR] [2018-12-13T00:24:43.520589Z] [s25608.local] [13881_1] [generateCandidateSV_0000] buildTime: 2018-04-26T23:54:06.820784Z

x-chen commented 5 years ago

duplicate with #164