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Structural variant and indel caller for mapped sequencing data
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Failed to complete command task: 'getAlignmentStats_generateStats_000' #274

Open zetamui opened 2 years ago

zetamui commented 2 years ago

I am running manta 1.6.0 with alignment output from STAR-Fusion's Aligned.out.sam after it is compressed to bam and sorted. The manta options for the configManta.py I used was

--rna --bam Aligned.out.sorted.bam --referenceFasta ~/Database/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa

My error is shown below:

[2021-10-18T03:16:13.255896Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/home/iblc3/Tools/manta-1.6.0.centos6_x86_64/libexec/GetAlignmentStats --ref /home/iblc3/Database/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa --output-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/MantaWorkflow/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/Aligned.out.sorted.bam'
[2021-10-18T03:16:13.349858Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 9 stderr lines from task (of 9 total lines):
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.772487Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2021-Oct-18 11:16:12 /builder/src/c++/lib/manta/ReadGroupStatsUtil.cpp(120): Throw in function int getFragSizeMinusSkip(const bam_record&)
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.807136Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException>
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.840562Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] std::exception::what: Unexpected fragment size (-7) deduced from bam record: NB501576:258:H2JK3AFX3:3:21512:21100:2559/1 tid:pos:strand 0:10072:+ cigar: 40M42N36M templSize: 35 mate_tid:pos:strand 0:10070:-
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.873952Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000]       Possible invalid template size in bam record.
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.907354Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000]
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.940762Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] cmdline:      /home/iblc3/Tools/manta-1.6.0.centos6_x86_64/libexec/GetAlignmentStats --ref /home/iblc3/Database/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa --output-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/MantaWorkflow/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/Aligned.out.sorted.bam
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:12.974120Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] version:      1.6.0
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:13.007538Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] buildTime:    2019-06-28T22:06:27.673004Z
[2021-10-18T03:16:13.424978Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] [2021-10-18T03:16:13.040929Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] compiler:     g++-6.3.1
[2021-10-18T03:16:13.500127Z] [Johnny-6] [18514_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2021-10-18T03:16:27.184213Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2021-10-18T03:16:27.258624Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/home/iblc3/Tools/manta-1.6.0.centos6_x86_64/libexec/GetAlignmentStats --ref /home/iblc3/Database/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa --output-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/MantaWorkflow/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/Aligned.out.sorted.bam'
[2021-10-18T03:16:27.372219Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 9 stderr lines from task (of 9 total lines):
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.772487Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2021-Oct-18 11:16:12 /builder/src/c++/lib/manta/ReadGroupStatsUtil.cpp(120): Throw in function int getFragSizeMinusSkip(const bam_record&)
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.807136Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException>
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.840562Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] std::exception::what: Unexpected fragment size (-7) deduced from bam record: NB501576:258:H2JK3AFX3:3:21512:21100:2559/1 tid:pos:strand 0:10072:+ cigar: 40M42N36M templSize: 35 mate_tid:pos:strand 0:10070:-
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.873952Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000]    Possible invalid template size in bam record.
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.907354Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000]
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.940762Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] cmdline:   /home/iblc3/Tools/manta-1.6.0.centos6_x86_64/libexec/GetAlignmentStats --ref /home/iblc3/Database/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa --output-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/MantaWorkflow/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/iblc3/MD/00_RNA-seq/01_featureCounts/21-IPCR-43-Swift-21MA033286-21S20959-I-16_S6_R1_001.fastq.gz_out/Aligned.out.sorted.bam
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:12.974120Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] version:   1.6.0
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:13.007538Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] buildTime: 2019-06-28T22:06:27.673004Z
[2021-10-18T03:16:27.439052Z] [Johnny-6] [18514_1] [WorkflowRunner] [ERROR] [2021-10-18T03:16:13.040929Z] [Johnny-6] [18514_1] [getAlignmentStats_generateStats_000] compiler:  g++-6.3.1

What exactly is wrong with that read shown in the error and how to rectify this?

voluptatis commented 2 years ago

I have met the same question, no matter use the pre-built release or built it by myself. Have you solved this issue?

nehasanghi commented 2 years ago

I am also facing the same issue though I have used the pre-built release only.Please help us recitfy this at earliest as I am running it on patients data and need to analyze it at earliest

My command is :

[2022-06-20T10:19:35.529095Z] [master.local] [205907_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignmentStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/storage/home/sgrh1/analysis_resources/SV_calling_data/manta-1.6.0.centos6_x86_64/libexec/GetAlignmentStats --ref /storage/goast/goast_data/hg19_public_data/Homo_sapiens_assembly19.fasta --output-file /storage/goast/goast_data/WGS_input/Rudrika_ghanti/manta/MantaWorkflow/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /storage/goast/cromwell_server/cromwell-slurm-exec/LenovoGenomeWorkflow/0adb7f05-23a7-497f-84dd-784b990de779/call-GatherBamFiles/execution/R.bam

jgarces02 commented 1 year ago

Me too. In my case, I'm working under a conda environment with manta's version 1.6.0 (within a HPC system).

workflow.warning.log.txt:

[2023-01-18T08:28:16.507761Z] [nodo05.xcat.local] [72325_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignm
entStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/jgarces/.
conda/envs/wes_env/share/manta-1.6.0-2/libexec/GetAlignmentStats --ref /home/jgarces/genomes/GRCh38.p13/GRCh38.p13.genome.fa --output-f
ile /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_SP_manta_res/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml
--align-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam'
[2023-01-18T08:29:46.726281Z] [nodo05.xcat.local] [72325_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignm
entStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/jgarces/.
conda/envs/wes_env/share/manta-1.6.0-2/libexec/GetAlignmentStats --ref /home/jgarces/genomes/GRCh38.p13/GRCh38.p13.genome.fa --output-f
ile /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_SP_manta_res/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml
--align-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam'

workflow.error.log.txt:

[2023-01-18T08:31:17.100312Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/home/jgarces/.conda/envs/wes_env/share/manta-1.6.0-2/libexec/GetAlignmentStats --ref /home/jgarces/genomes/GRCh38.p13/GRCh38.p13.genome.fa --output-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_SP_manta_res/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam'
[2023-01-18T08:31:17.150661Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 15 stderr lines from task (of 15 total lines):
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.014426Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2023-Jan-18 09:31:17 /builder/src/c++/lib/manta/ReadGroupStatsUtil.cpp(210): Throw in function void ReadGroupOrientTracker::finalize(const ReadCounter&)
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.015691Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException>
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.016669Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] std::exception::what: Too few high-confidence read pairs (0) to determine pair orientation for read group '' in bam file '/home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam'
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.017643Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]     At least 100 high-confidence read pairs are required to determine pair orientation.
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.018581Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]     Total sampled reads: 0
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.019939Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]     Total sampled paired reads: 0
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.020916Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]     Total sampled paired reads passing MAPQ filter: 0
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.021857Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]     Total sampled high-confidence read pairs passing all filters: 0
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.022777Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.044033Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.044983Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.045899Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] cmdline:    /home/jgarces/.conda/envs/wes_env/share/manta-1.6.0-2/libexec/GetAlignmentStats --ref /home/jgarces/genomes/GRCh38.p13/GRCh38.p13.genome.fa --output-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_SP_manta_res/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.046843Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] version:    1.6.0
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.047738Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] buildTime:  2019-06-28T22:06:27.673004Z
[2023-01-18T08:31:17.153341Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] [2023-01-18T08:31:17.048668Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] compiler:   g++-6.3.1
[2023-01-18T08:31:17.208418Z] [nodo05.xcat.local] [72325_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2023-01-18T08:31:29.459998Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2023-01-18T08:31:29.462837Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/home/jgarces/.conda/envs/wes_env/share/manta-1.6.0-2/libexec/GetAlignmentStats --ref /home/jgarces/genomes/GRCh38.p13/GRCh38.p13.genome.fa --output-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_SP_manta_res/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam'
[2023-01-18T08:31:29.465644Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 15 stderr lines from task (of 15 total lines):
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.014426Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2023-Jan-18 09:31:17 /builder/src/c++/lib/manta/ReadGroupStatsUtil.cpp(210): Throw in function void ReadGroupOrientTracker::finalize(const ReadCounter&)
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.015691Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException>
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.016669Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] std::exception::what: Too few high-confidence read pairs (0) to determine pair orientation for read group '' in bam file '/home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam'
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.017643Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]  At least 100 high-confidence read pairs are required to determine pair orientation.
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.018581Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]  Total sampled reads: 0
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.019939Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]  Total sampled paired reads: 0
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.020916Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]  Total sampled paired reads passing MAPQ filter: 0
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.021857Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]  Total sampled high-confidence read pairs passing all filters: 0
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.022777Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.044033Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.044983Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000]
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.045899Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] cmdline: /home/jgarces/.conda/envs/wes_env/share/manta-1.6.0-2/libexec/GetAlignmentStats --ref /home/jgarces/genomes/GRCh38.p13/GRCh38.p13.genome.fa --output-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_SP_manta_res/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/jgarces/projects/GEMRNA.WES/data/processed/738-2_LT.sorted.bam
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.046843Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] version: 1.6.0
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.047738Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] buildTime:   2019-06-28T22:06:27.673004Z
[2023-01-18T08:31:29.468378Z] [nodo05.xcat.local] [72325_1] [WorkflowRunner] [ERROR] [2023-01-18T08:31:17.048668Z] [nodo05.xcat.local] [72325_1] [getAlignmentStats_generateStats_000] compiler:    g++-6.3.1

Thanks