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Illumina / manta

Structural variant and indel caller for mapped sequencing data
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Failed to complete command task: 'generateCandidateSV_0000' #216

Open azzatha opened 4 years ago

azzatha commented 4 years ago

Greetings,

I got the following errors with some real samples I have, not sure about the source of the error as the BAM files generated successfully, any advice?

[2020-02-25T23:07:54.845014Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [TaskManager] [ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1, command: '/sw/csi/manta/1.6/el7.6_binary/manta-1.6.0.centos6_x86_64/libexec/GenerateSVCandidates --threads 40 --align-stats ./workspace/alignmentStats.xml --graph-file ./workspace/svLocusGraph.bin --bin-index 0 --bin-count 1 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref Homo_sapiens_assembly38.fasta --candidate-output-file /workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /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 /workspace/chromDepth.txt --edge-runtime-log 170608/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /results/stats/svCandidateGenerationStats.xml --edge-stats-report /results/stats/svCandidateGenerationStats.tsv --align-file 170608.sorted.bam' [2020-02-25T23:07:54.857735Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Error Message: [2020-02-25T23:07:54.858360Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Last 19 stderr lines from task (of 19 total lines): [2020-02-25T23:07:54.858360Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [TaskManager] [ERROR] [2020-02-25T23:07:54.795090Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [generateCandidateSV_0000] FATAL_ERROR: 2020-Feb-26 02:07:54 /builder/src/c++/lib/manta/SVCandidateSetData.cpp(125): Throw in function void SVCandidateSetSequenceFragmentSampleGroup::add(const bam_header_info&, const bam_record&, bool, bool, bool) .... .... .... ... 6_1] [generateCandidateSV_0000] cmdline: /sw/csi/manta/1.6/el7.6_binary/manta-1.6.0.centos6_x86_64/libexec/GenerateSVCandidates --threads 40 --align-stats /workspace/alignmentStats.xml --graph-file /workspace/svLocusGraph.bin --bin-index 0 --bin-count 1 --max-edge-count 10 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-size 50 --ref Homo_sapiens_assembly38.fasta --candidate-output-file /workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /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 /workspace/chromDepth.txt --edge-runtime-log /workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log/results/stats/svCandidateGenerationStats.xml --edge-stats-report 170608/results/stats/svCandidateGenerationStats.tsv --align-file 170608.sorted.bam [2020-02-25T23:08:04.485482Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [WorkflowRunner] [ERROR] [2020-02-25T23:07:54.800679Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [generateCandidateSV_0000] version: 1.6.0 [2020-02-25T23:08:04.485482Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [WorkflowRunner] [ERROR] [2020-02-25T23:07:54.800861Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [generateCandidateSV_0000] buildTime: 2019-06-28T22:06:27.673004Z [2020-02-25T23:08:04.485482Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [WorkflowRunner] [ERROR] [2020-02-25T23:07:54.801042Z] [cn603-04-r.ibex.kaust.edu.sa] [258266_1] [generateCandidateSV_0000] compiler: g++-6.3.1

Thank you,

TylerMclaughlin commented 3 years ago

I too am getting this fatal error. FATAL_ERROR: 2020-Oct-13 21:08:36 /builder/src/c++/lib/manta/SVCandidateSetData.cpp(157): Throw in function void SVCandidateSetSequenceFragmentSampleGroup::add(const bam_header_info&, const bam_record&, bool, bool, bool)

pkMyt1 commented 3 years ago

Anyone have a solution for this? I am just starting with manta and get the same error but the demo data works fine

fayina commented 3 years ago

I am just getting the same error, anyone have a solution?

pkMyt1 commented 3 years ago

I think this error is a bit general. I found the root cause of mine buried in one of the log files, it was never displayed. For me it is a name collision. I had to merge three lanes from a Novoseq S4 to generate my data. Because of the way the names are read (lane number is ignored), some are the same now. To change the behavior of manta would require changing one or more of the C files and recompiling, something I am not really willing to do. My work around is to run manta on groups of chromosomes so that the reads with the same names are never in the same run.