[ERROR] Failed to complete command task: 'generateCandidateSV_0000' , error code: 1 in germline samples analysis
HZAUzyz opened this issue · 1 comments
Hi,
I have run the manta 1.6.0 for germlines analysis.
Here is my commands:
#configuration
python2 {path_to_manta}/bin/configManta.py --bam my_sample.sorted.markdup.bam --reference /path_to_my_reference_genome/genome.chromosome.fa --runDir .
#Excution
python2 runWorkflow.py -j 20
After I run configuration successfully, I got runWorkflow.py, and it works well in almost samples, while in several samples ,there are some ERROR and stop.
Here is the workflow.err.log.txt:
Maybe the error is "Throw infunction void processEdge"? I'm confused about this
[2021-09-07T11:19:36.009814Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] Failed to complete command task: 'generateCandidateSV_0000' launched from master workflow, error code: 1, command: '/home/Tools/manta-1.6.0.centos6_x86_64/libexec/GenerateSVCandidates --threads 40 --align-stats /manta/8L/workspace/alignmentStats.xml --graph-file /manta/8L/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 /home/01_DATA-Genome/HWB.chromosome.fa --candidate-output-file /manta/8L/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /manta/8L/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 /manta/8L/workspace/chromDepth.txt --edge-runtime-log /manta/8L/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /manta/8L/results/stats/svCandidateGenerationStats.xml --edge-stats-report /manta/8L/results/stats/svCandidateGenerationStats.tsv --align-file /out_bam/8L.sorted.markdup.bam'
[2021-09-07T11:19:36.011789Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Error Message:
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [generateCandidateSV_0000] Last 40 stderr lines from task (of 164 total lines):
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:30.497893Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000]
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:30.498348Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000]
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.937873Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] FATAL_ERROR: 2021-Sep-07 19:19:35 /builder/src/c++/lib/applications/GenerateSVCandidates/GenerateSVCandidates.cpp(193): Throw infunction void processEdge(int, const GSCOptions&, const SVLocusSet&, std::vector&, EdgeInfo)
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.938490Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] Dynamic exception type: boost::exception_detail::clone_implillumina::common::GeneralException
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.938967Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] std::exception::what: Attempting to lookup basecallquality score 72 which exceeds the maximum cached basecall quality score of 70
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.939237Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] [processEdge(int, GSCOptions const&, SVLocusSet const&, std::vector<EdgeThreadLocalData, std::allocator >&,EdgeInfo)::current_edge_info*] = Exception caught in thread 35 while processing graph edge: edgeinfo locus:node1:node2: 1:5:51773
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.939417Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] node1:LocusNode: GenomeInterval: 3:[16485612,16488897) n_edges: 22 out_count: 1257 evidence: [16485792,16488856)
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.939652Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] EdgeTo: 3 out_count: 0
[2021-09-07T11:19:36.012753Z] [localhost.localdomain] [138836_1] [TaskManager] [ERROR] [2021-09-07T11:19:35.939889Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] EdgeTo: 5 out_count: 336
Beside, here is the informations in pyflow_tasks_stderr_log.txt:
pyflow_tasks_stderr_log.txt
[2021-09-07T11:16:22.709474Z] [localhost.localdomain] [138836_1] [generateCan
didateSV_0000] cmdline: /home/Tools/manta-1.6.0.centos6_x86_64/libexec/Gen
erateSVCandidates --threads 40 --align-stats /manta/8L/workspace/alignmentStats.xml --grap
h-file /manta/8L/workspace/svLocusGraph.bin --bin-index 0 --bin-count 1 --max-edge-count 1
0 --min-candidate-sv-size 8 --min-candidate-spanning-count 3 --min-scored-sv-
size 50 --ref /home/01_DATA-Genome/HWB/HWB.chromosome.fa --candidate-output-f
ile /manta/8L/workspace/svHyGen/candidateSV.0000.vcf --diploid-output-file /manta/8L/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 /manta/8L/workspace/chromDepth.txt
--edge-runtime-log /manta/8L/workspace/svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log /manta/8L/resul
ts/stats/svCandidateGenerationStats.xml --edge-stats-report /manta/8L/results/stats/svCand
idateGenerationStats.tsv --align-file //out_bam/8L.sorted.markdup.bam
[2021-09-07T11:16:22.709664Z] [localhost.localdomain] [138836_1] [generateCan
didateSV_0000] version: 1.6.0
[2021-09-07T11:16:22.709843Z] [localhost.localdomain] [138836_1] [generateCan
didateSV_0000] buildTime: 2019-06-28T22:06:27.673004Z
[2021-09-07T11:16:22.710020Z] [localhost.localdomain] [138836_1] [generateCan
didateSV_0000] compiler: g++-6.3.1
[2021-09-07T11:16:22.740572Z] [localhost.localdomain] [138836_1] [pyflowTaskW
rapper:generateCandidateSV_0000] Task: 'generateCandidateSV_0000' exit code:
'1'
[2021-09-07T11:17:53.799465Z] [localhost.localdomain] [138836_1] [generateCan
didateSV_0000] ERROR: Exception caught in getReadSplitScore() while scoring read: FCC2UEKACXX:4:2104:15403:30032#/2 tid:pos:strand 8:5609465:+ cigar: 90MtemplSize: 0 mate_tid:pos:strand 5:3151162:-
[2021-09-07T11:17:53.800213Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] Exception caught while attempting to score SVCandidate:
[2021-09-07T11:17:53.801214Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] isImprecise?: 0
[2021-09-07T11:17:53.802293Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] forwardTranscriptStrandReadCount: 6 ; reverseTranscriptStrandReadCount: 5
[2021-09-07T11:17:53.802812Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] index candidate:assemblyAlign:assemblySegment: 0:2:0
[2021-09-07T11:17:53.803282Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] Alignment:
[2021-09-07T11:17:53.803736Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] BreakendInsertSeq: AC
[2021-09-07T11:17:53.804187Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] Breakend: GenomeInterval: 8:[5609553,5609554) RIGHT_OPEN
[2021-09-07T11:17:53.804759Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000] SVBreakendLowResEvidence: pair: 5 local_pair: 11 cigar: 0softclip: 0 semialign: 0 shadow: 0 split_align: 0 unknown: 0
[2021-09-07T11:17:53.805231Z] [localhost.localdomain] [138836_1] [generateCandidateSV_0000]
I have tried to rerun the same input, and still failed, and I can't find the same error in other issues, I can't figure it out.
In addition, I have more than 100 samples running succesfully, and four samples error, , they all running the same pipeline.
Thanks for your time and looking forward to your reply. @x-chen @ctsa
I have found the reason why I failed running some samples, and shared to anyone who might meet the same error issue.
Please check the fastq quatlity format, if you use phred64 fastq as input and mapped to the reference, it might be failed, transferred to phred33 by seqtk will solve the problem（https://github.com/lh3/seqtk）