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Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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[ERROR] 'generateCandidateSV_0000' error code: 1 #276

Closed zhiyongli1995 closed 2 years ago

zhiyongli1995 commented 2 years ago

Here is my error log file, hope for answers!!!

[2021-10-20T09:43:14.202845Z] [cu01] [38908_1] [TaskManager] **[ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1**, command: '/home/root/miniconda3/envs/python27/share/manta-1.6.0-1/libexec/GenerateSVCandidates --threads 80 --align-stats /xincunchu/CallSV/SyRI/manta/workspace/alignmentStats.xml --graph-file /xincunchu/CallSV/SyRI/manta/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 /xincunchu/XIANSHI/reference/b73v4r41.fa --candidate-output-file /xincunchu/CallSV/SyRI/manta/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /xincunchu/CallSV/SyRI/manta/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 /xincunchu/CallSV/SyRI/manta/workspace/chromDepth.txt --edge-runtime-log /xincunchu/CallSV/SyRI/manta/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /xincunchu/CallSV/SyRI/manta/results/stats/svCandidateGenerationStats.xml --edge-stats-report /xincunchu/CallSV/SyRI/manta/results/stats/svCandidateGenerationStats.tsv --align-file /xincunchu/XIANSHI/pipline/bam/NC358.sort.dup.head.bam'
[2021-10-20T09:43:14.328010Z] [cu01] [38908_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Error Message:
[2021-10-20T09:43:14.428062Z] [cu01] [38908_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Anomalous task wrapper stderr output. Wrapper signal file: '/xincunchu/CallSV/SyRI/manta/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/448/pyflowTaskWrapper.signal.txt'
[2021-10-20T09:43:14.486364Z] [cu01] [38908_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Logging 2 line(s) of task wrapper log output below:
[2021-10-20T09:43:14.561380Z] [cu01] [38908_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-10-20T07:16:16.759515Z] [cu01] [38908_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] wrapperStart
[2021-10-20T09:43:14.611350Z] [cu01] [38908_1] [TaskManager] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-10-20T07:16:16.817555Z] [cu01] [38908_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] taskStart
[2021-10-20T09:43:14.686355Z] [cu01] [38908_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2021-10-20T09:43:23.645355Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2021-10-20T09:43:23.718172Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1, command: '/home/root/miniconda3/envs/python27/share/manta-1.6.0-1/libexec/GenerateSVCandidates --threads 80 --align-stats /xincunchu/CallSV/SyRI/manta/workspace/alignmentStats.xml --graph-file /xincunchu/CallSV/SyRI/manta/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 /xincunchu/XIANSHI/reference/b73v4r41.fa --candidate-output-file /xincunchu/CallSV/SyRI/manta/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /xincunchu/CallSV/SyRI/manta/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 /xincunchu/CallSV/SyRI/manta/workspace/chromDepth.txt --edge-runtime-log /xincunchu/CallSV/SyRI/manta/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /xincunchu/CallSV/SyRI/manta/results/stats/svCandidateGenerationStats.xml --edge-stats-report /xincunchu/CallSV/SyRI/manta/results/stats/svCandidateGenerationStats.tsv --align-file /xincunchu/XIANSHI/pipline/bam/NC358.sort.dup.head.bam'
[2021-10-20T09:43:23.784903Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] Error Message:
[2021-10-20T09:43:23.859869Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] Anomalous task wrapper stderr output. Wrapper signal file: '/xincunchu/CallSV/SyRI/manta/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/448/pyflowTaskWrapper.signal.txt'
[2021-10-20T09:43:23.943199Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] Logging 2 line(s) of task wrapper log output below:
[2021-10-20T09:43:24.026508Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-10-20T07:16:16.759515Z] [cu01] [38908_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] wrapperStart
[2021-10-20T09:43:24.076521Z] [cu01] [38908_1] [WorkflowRunner] [ERROR] [generateCandidateSV_0000] [taskWrapper-stderr] [2021-10-20T07:16:16.817555Z] [cu01] [38908_1] [pyflowTaskWrapper:generateCandidateSV_0000] [wrapperSignal] taskStart
zhiyongli1995 commented 2 years ago

Hi, I solved this problem by switching over the python environment version (from python3.8 to python2.7).