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Illumina / manta

Structural variant and indel caller for mapped sequencing data
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Does Manta support 10x linked-read sorted bam files? #280

Open goldpm1 opened 2 years ago

goldpm1 commented 2 years ago

Hi.

I'm using 10x linked-read pipeline and acquired bam files through LongRanger tool.

I'm trying to apply Manta 1.6.0 for these bam files, but the error has occured. I looked upon similar articles about this error, but unlike those, it seems not a memory problem, python version or Manta version, because other Bam files (Illumina or BGI seq) run without problem. (I used GRCh38 reference files provided by 10X genomics on this linked-read bam files)

Below is my code and error message. Thank you.

python /opt/Yonsei/Manta/1.6.0/bin/configManta.py \
        --referenceFasta "/data/public/LongRanger/GRCh38_2.1.0/fasta/genome.fa"  \
        --bam /data/project/craniosynostosis/0.raw/0.bam/CR.3.bam \
        --runDir /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3 \
        --generateEvidenceBam

python /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/runWorkflow.py -j 28
> [2021-12-03T15:50:40.102568Z] [compute03] [267809_1] [TaskManager] [ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1, command: '/opt/Yonsei/Manta/1.6.0/libexec/GenerateSVCandidates --threads 28 --align-stats /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/alignmentStats.xml --graph-file [/data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svLocusGraph.bin](url) --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 /data/public/LongRanger/GRCh38_2.1.0/fasta/genome.fa --candidate-output-file /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/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 /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/chromDepth.txt --edge-runtime-log /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/results/stats/svCandidateGenerationStats.xml --edge-stats-report /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/results/stats/svCandidateGenerationStats.tsv --evidence-bam-stub /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svHyGen/evidence_0000 --align-file /data/project/craniosynostosis/0.raw/0.bam/CR.3.bam'
> [2021-12-03T15:50:40.131512Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Error Message:
> [2021-12-03T15:50:40.141822Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Anomalous task wrapper stderr output. Wrapper signal file: '/data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/431/pyflowTaskWrapper.signal.txt'
> [2021-12-03T15:50:40.151795Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Logging 5 line(s) of task wrapper log output below:
> [2021-12-03T15:50:40.161034Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-12-03T15:49:32.901042Z] [compute03] [267809_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] wrapperStart
> [2021-12-03T15:50:40.171021Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-12-03T15:49:33.001644Z] [compute03] [267809_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] taskStart
> [2021-12-03T15:50:40.180805Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-12-03T15:50:40.022339Z] [compute03] [267809_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] taskExitCode -11
> [2021-12-03T15:50:40.190109Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-12-03T15:50:40.049525Z] [compute03] [267809_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] taskStderrTail 1
> [2021-12-03T15:50:40.200112Z] [compute03] [267809_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
> [2021-12-03T15:50:40.209729Z] [compute03] [267809_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
> [2021-12-03T15:50:46.777041Z] [compute03] [267809_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
> [2021-12-03T15:50:46.800284Z] [compute03] [267809_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1, command: '/opt/Yonsei/Manta/1.6.0/libexec/GenerateSVCandidates --threads 28 --align-stats /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/alignmentStats.xml --graph-file /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/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 /data/public/LongRanger/GRCh38_2.1.0/fasta/genome.fa --candidate-output-file /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/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 /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/chromDepth.txt --edge-runtime-log /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/results/stats/svCandidateGenerationStats.xml --edge-stats-report /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/results/stats/svCandidateGenerationStats.tsv --evidence-bam-stub /data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/svHyGen/evidence_0000 --align-file /data/project/craniosynostosis/0.raw/0.bam/CR.3.bam'
> [2021-12-03T15:50:46.810930Z] [compute03] [267809_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] Error Message:
> [2021-12-03T15:50:46.821474Z] [compute03] [267809_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] Anomalous task wrapper stderr output. Wrapper signal file: '/data/project/craniosynostosis/8.SV/manta/1.raw/CR.3/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/431/pyflowTaskWrapper.signal.txt'
> [2021-12-03T15:50:46.831134Z] [compute03] [267809_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] Logging 5 line(s) of task wrapper log output below:
> [2021-12-03T15:50:46.840183Z] [compute03] [267809_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr]

manta_CR.3.txt

distilledchild commented 1 year ago

@goldpm1 Hi, were you successful to run this tool with linked-read from 10X genomics ?? I

ValentinaBoP commented 1 year ago

@goldpm1 @distilledchild I also experienced the same issue with linked reads but I noticed that SVs get called but Manta gets stuck when generating the BAM files (--generateEvidenceBam). If you remove that option then it works fine. I suspect that by removing some tags from the input BAM file and make it look more like a BAM from bwa then the --generateEvidenceBam option should work (I still need to test this).

distilledchild commented 1 year ago

@ValentinaBoP Thank you for your tip!