Created
October 26, 2017 10:36
-
-
Save MBeyens/f5869c46d42d824429078afffebb9c30 to your computer and use it in GitHub Desktop.
cnvkit segmentation fault
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [2017-10-26T09:46Z] System YAML configuration: /mnt/home_nfs1/mbeyens/local/share/bcbio/galaxy/bcbio_system.yaml | |
| [2017-10-26T09:46Z] Resource requests: sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16 | |
| [2017-10-26T09:46Z] Configuring 3 jobs to run, using 16 cores each with 32.1g of memory reserved for each job | |
| [2017-10-26T09:46Z] Timing: organize samples | |
| [2017-10-26T09:46Z] multiprocessing: organize_samples | |
| [2017-10-26T09:46Z] Using input YAML configuration: /home/mbeyens/WGS_data/pair_analysis_1/config/run_paired_config.yaml | |
| [2017-10-26T09:46Z] Checking sample YAML configuration: /home/mbeyens/WGS_data/pair_analysis_1/config/run_paired_config.yaml | |
| [2017-10-26T09:46Z] Testing minimum versions of installed programs | |
| [2017-10-26T09:47Z] Timing: alignment preparation | |
| [2017-10-26T09:47Z] multiprocessing: prep_align_inputs | |
| [2017-10-26T09:47Z] multiprocessing: disambiguate_split | |
| [2017-10-26T09:47Z] Timing: alignment | |
| [2017-10-26T09:47Z] multiprocessing: process_alignment | |
| [2017-10-26T09:47Z] Timing: callable regions | |
| [2017-10-26T09:47Z] multiprocessing: prep_samples | |
| [2017-10-26T09:47Z] multiprocessing: postprocess_alignment | |
| [2017-10-26T09:47Z] 161620: Assigned coverage as 'genome' with 89.8% genome coverage and 0.0% offtarget coverage | |
| [2017-10-26T09:47Z] 161624: Assigned coverage as 'genome' with 89.3% genome coverage and 0.0% offtarget coverage | |
| [2017-10-26T09:47Z] 161619: Assigned coverage as 'genome' with 89.7% genome coverage and 0.0% offtarget coverage | |
| [2017-10-26T09:47Z] 161623: Assigned coverage as 'genome' with 89.2% genome coverage and 0.0% offtarget coverage | |
| [2017-10-26T09:47Z] multiprocessing: combine_sample_regions | |
| [2017-10-26T09:47Z] Identified 249 parallel analysis blocks | |
| Block sizes: | |
| min: 4262 | |
| 5%: 36247.2 | |
| 25%: 1920597.0 | |
| median: 16078400.0 | |
| 75%: 17607373.0 | |
| 95%: 22972699.0 | |
| 99%: 34057170.36 | |
| max: 36763413 | |
| Between block sizes: | |
| min: 253 | |
| 5%: 267.0 | |
| 25%: 315.0 | |
| median: 475.5 | |
| 75%: 1035.0 | |
| 95%: 25684.0 | |
| 99%: 10000000.0 | |
| max: 10000000 | |
| [2017-10-26T09:47Z] multiprocessing: calculate_sv_bins | |
| [2017-10-26T09:47Z] multiprocessing: calculate_sv_coverage | |
| [2017-10-26T09:47Z] Timing: hla typing | |
| [2017-10-26T09:47Z] Resource requests: freebayes, gatk, gatk-haplotype, mutect2, picard, vardict, varscan; memory: 2.00, 3.50, 2.00, 2.00, 2.00, 2.00, 2.00; cores: 16, 1, 16, 16, 16, 16, 16 | |
| [2017-10-26T09:47Z] Configuring 48 jobs to run, using 1 cores each with 3.50g of memory reserved for each job | |
| [2017-10-26T09:47Z] Timing: alignment post-processing | |
| [2017-10-26T09:47Z] multiprocessing: piped_bamprep | |
| [2017-10-26T09:47Z] Timing: variant calling | |
| [2017-10-26T09:47Z] multiprocessing: variantcall_sample | |
| [2017-10-26T09:49Z] multiprocessing: concat_variant_files | |
| [2017-10-26T09:49Z] Resource requests: bcbio_variation, fastqc, gatk, gatk-vqsr, gemini, kraken, preseq, qsignature, sambamba, samtools, snpeff; memory: 2.00, 2.00, 3.50, 2.00, 2.00, 2.00, 2.00, 2.00, 2.00, 2.00, 4.00; cores: 16, 16, 1, 16, 16, 16, 16, 16, 16, 16, 1 | |
| [2017-10-26T09:49Z] Configuring 2 jobs to run, using 16 cores each with 64.1g of memory reserved for each job | |
| [2017-10-26T09:49Z] Timing: joint squaring off/backfilling | |
| [2017-10-26T09:49Z] Timing: variant post-processing | |
| [2017-10-26T09:49Z] multiprocessing: postprocess_variants | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161620, varscan | |
| [2017-10-26T09:49Z] Calculating variation effects for 161620, varscan | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161624, mutect2 | |
| [2017-10-26T09:49Z] Calculating variation effects for 161624, mutect2 | |
| [2017-10-26T09:49Z] Annotate VCF file: 161620, varscan | |
| [2017-10-26T09:49Z] Filtering for 161620, varscan | |
| [2017-10-26T09:49Z] Prioritization for 161620, varscan | |
| [2017-10-26T09:49Z] Annotate VCF file: 161624, mutect2 | |
| [2017-10-26T09:49Z] Filtering for 161624, mutect2 | |
| [2017-10-26T09:49Z] Prioritization for 161624, mutect2 | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161620, gatk-haplotype | |
| [2017-10-26T09:49Z] Calculating variation effects for 161620, gatk-haplotype | |
| [2017-10-26T09:49Z] Annotate VCF file: 161620, gatk-haplotype | |
| [2017-10-26T09:49Z] Filtering for 161620, gatk-haplotype | |
| [2017-10-26T09:49Z] Skipping VQSR, using cutoff-based filers: we don't have whole genome input data | |
| [2017-10-26T09:49Z] Prioritization for 161620, gatk-haplotype | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161620, mutect2 | |
| [2017-10-26T09:49Z] Calculating variation effects for 161620, mutect2 | |
| [2017-10-26T09:49Z] Annotate VCF file: 161620, mutect2 | |
| [2017-10-26T09:49Z] Filtering for 161620, mutect2 | |
| [2017-10-26T09:49Z] Prioritization for 161620, mutect2 | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161620, vardict | |
| [2017-10-26T09:49Z] Calculating variation effects for 161620, vardict | |
| [2017-10-26T09:49Z] Annotate VCF file: 161620, vardict | |
| [2017-10-26T09:49Z] Filtering for 161620, vardict | |
| [2017-10-26T09:49Z] Prioritization for 161620, vardict | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161624, vardict | |
| [2017-10-26T09:49Z] Calculating variation effects for 161624, vardict | |
| [2017-10-26T09:49Z] Annotate VCF file: 161624, vardict | |
| [2017-10-26T09:49Z] Filtering for 161624, vardict | |
| [2017-10-26T09:49Z] Prioritization for 161624, vardict | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161624, gatk-haplotype | |
| [2017-10-26T09:49Z] Calculating variation effects for 161624, gatk-haplotype | |
| [2017-10-26T09:49Z] Annotate VCF file: 161624, gatk-haplotype | |
| [2017-10-26T09:49Z] Filtering for 161624, gatk-haplotype | |
| [2017-10-26T09:49Z] Prioritization for 161624, gatk-haplotype | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161624, freebayes | |
| [2017-10-26T09:49Z] Calculating variation effects for 161624, freebayes | |
| [2017-10-26T09:49Z] Annotate VCF file: 161624, freebayes | |
| [2017-10-26T09:49Z] Filtering for 161624, freebayes | |
| [2017-10-26T09:49Z] Prioritization for 161624, freebayes | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161620, freebayes | |
| [2017-10-26T09:49Z] Calculating variation effects for 161620, freebayes | |
| [2017-10-26T09:49Z] Annotate VCF file: 161620, freebayes | |
| [2017-10-26T09:49Z] Filtering for 161620, freebayes | |
| [2017-10-26T09:49Z] Prioritization for 161620, freebayes | |
| [2017-10-26T09:49Z] Finalizing variant calls: 161624, varscan | |
| [2017-10-26T09:49Z] Calculating variation effects for 161624, varscan | |
| [2017-10-26T09:49Z] Annotate VCF file: 161624, varscan | |
| [2017-10-26T09:49Z] Filtering for 161624, varscan | |
| [2017-10-26T09:49Z] Prioritization for 161624, varscan | |
| [2017-10-26T09:49Z] multiprocessing: split_variants_by_sample | |
| [2017-10-26T09:49Z] Timing: prepped BAM merging | |
| [2017-10-26T09:49Z] Timing: validation | |
| [2017-10-26T09:49Z] multiprocessing: compare_to_rm | |
| [2017-10-26T09:50Z] Timing: ensemble calling | |
| [2017-10-26T09:50Z] Timing: validation summary | |
| [2017-10-26T09:50Z] Timing: structural variation precall | |
| [2017-10-26T09:50Z] Timing: structural variation | |
| [2017-10-26T09:50Z] Timing: structural variation | |
| [2017-10-26T09:50Z] Timing: structural variation ensemble | |
| [2017-10-26T09:50Z] Timing: structural variation validation | |
| [2017-10-26T09:50Z] multiprocessing: validate_sv | |
| [2017-10-26T09:50Z] Timing: heterogeneity | |
| [2017-10-26T09:50Z] Timing: population database | |
| [2017-10-26T09:50Z] multiprocessing: prep_gemini_db | |
| [2017-10-26T09:50Z] Timing: quality control | |
| [2017-10-26T09:50Z] multiprocessing: pipeline_summary | |
| [2017-10-26T09:50Z] QC: 161624 fastqc | |
| [2017-10-26T09:50Z] QC: 161624 qualimap | |
| [2017-10-26T09:50Z] Downsample BAM file: 161624-dedup.bam | |
| [2017-10-26T09:50Z] Downsample BAM file: 161624-dedup.bam | |
| [2017-10-26T10:21Z] FastQC: 161624 | |
| [2017-10-26T10:21Z] Prepare merged BED file : 161624 | |
| [2017-10-26T10:21Z] bgzip 161624-coverage.callable-vrsubset-callableblocks-merged-merged.bed | |
| [2017-10-26T10:21Z] tabix index 161624-coverage.callable-vrsubset-callableblocks-merged-merged.bed.gz | |
| [2017-10-26T10:21Z] Qualimap: 161624 | |
| [2017-10-26T10:21Z] Display: | |
| [2017-10-26T10:21Z] Java memory size is set to 59g | |
| [2017-10-26T10:21Z] Launching application... | |
| [2017-10-26T10:21Z] Started analysis of 161624-dedup-downsample.bam | |
| [2017-10-26T10:21Z] QualiMap v.2.2.2-dev | |
| [2017-10-26T10:21Z] Built on 2016-12-11 14:41 | |
| [2017-10-26T10:21Z] Selected tool: bamqc | |
| [2017-10-26T10:21Z] Available memory (Mb): 32 | |
| [2017-10-26T10:21Z] Max memory (Mb): 56312 | |
| [2017-10-26T10:21Z] Thu Oct 26 12:21:05 CEST 2017 WARNING Output folder already exists, the results will be saved there | |
| [2017-10-26T10:21Z] Starting bam qc.... | |
| [2017-10-26T10:21Z] Loading sam header... | |
| [2017-10-26T10:21Z] Loading locator... | |
| [2017-10-26T10:21Z] Loading reference... | |
| [2017-10-26T10:21Z] Only flagged duplicate alignments will be skipped... | |
| [2017-10-26T10:21Z] Number of windows: 400, effective number of windows: 492 | |
| [2017-10-26T10:21Z] Chunk of reads size: 1000 | |
| [2017-10-26T10:21Z] Number of threads: 16 | |
| 282 | |
| [2017-10-26T10:21Z] Initializing regions from /mnt/home_nfs1/mbeyens/WGS_data/pair_analysis_1/work/qc/161624/qualimap/161624-coverage.callable-vrsubset-callableblocks-merged-merged-bed6.bed..... | |
| cmd) | |
| ---> 23 _do_run(cmd, checks, log_stdout, env=env) | |
| cmd = 'unset R_HOME && unset R_LIBS && export PATH=/mnt..._analysis/work/mutect2/1-effects-annotated.vcf.gz' | |
| checks = None | |
| log_stdout = False | |
| env = None | |
| 24 except: | |
| 25 diagnostics.end_cmd(cmd_id, False) | |
| 26 if log_error: | |
| 27 logger.exception() | |
| ........................................................................... | |
| /home/mbeyens/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py in _do_run(cmd='set -o pipefail; unset R_HOME && unset R_LIBS &&..._analysis/work/mutect2/1-effects-annotated.vcf.gz', checks=None, log_stdout=False, env=None) | |
| 98 error_msg = " ".join(cmd) if not isinstance(cmd, basestring) else cmd | |
| 99 error_msg += "\n" | |
| 100 error_msg += "".join(debug_stdout) | |
| 101 s.communicate() | |
| 102 s.stdout.close() | |
| --> 103 raise subprocess.CalledProcessError(exitcode, error_msg) | |
| exitcode = 139 | |
| error_msg = 'set -o pipefail; unset R_HOME && unset R_LIBS &&...analysis/work/mutect2/1-effects-annotated.vcf.gz\n' | |
| 104 else: | |
| 105 break | |
| 106 s.communicate() | |
| 107 s.stdout.close() | |
| CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin:$PATH && export TMPDIR=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7 && /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| Selected test sample P00132893_tumor and control sample P00132893_normal | |
| /bin/bash: line 1: 65589 Segmentation fault (core dumped) /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| ' returned non-zero exit status 139 | |
| ___________________________________________________________________________ | |
| ---> 23 _do_run(cmd, checks, log_stdout, env=env) | |
| cmd = 'unset R_HOME && unset R_LIBS && export PATH=/mnt..._analysis/work/mutect2/1-effects-annotated.vcf.gz' | |
| checks = None | |
| log_stdout = False | |
| env = None | |
| 24 except: | |
| 25 diagnostics.end_cmd(cmd_id, False) | |
| 26 if log_error: | |
| 27 logger.exception() | |
| ........................................................................... | |
| /home/mbeyens/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py in _do_run(cmd='set -o pipefail; unset R_HOME && unset R_LIBS &&..._analysis/work/mutect2/1-effects-annotated.vcf.gz', checks=None, log_stdout=False, env=None) | |
| 98 error_msg = " ".join(cmd) if not isinstance(cmd, basestring) else cmd | |
| 99 error_msg += "\n" | |
| 100 error_msg += "".join(debug_stdout) | |
| 101 s.communicate() | |
| 102 s.stdout.close() | |
| --> 103 raise subprocess.CalledProcessError(exitcode, error_msg) | |
| exitcode = 139 | |
| error_msg = 'set -o pipefail; unset R_HOME && unset R_LIBS &&...analysis/work/mutect2/1-effects-annotated.vcf.gz\n' | |
| 104 else: | |
| 105 break | |
| 106 s.communicate() | |
| 107 s.stdout.close() | |
| CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin:$PATH && export TMPDIR=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7 && /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| Selected test sample P00132893_tumor and control sample P00132893_normal | |
| /bin/bash: line 1: 65589 Segmentation fault (core dumped) /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| ' returned non-zero exit status 139 | |
| ___________________________________________________________________________ | |
| mbeyens@trainingvm-n001:/home/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work$ | |
| mbeyens@trainingvm-n001:/home/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work$ | |
| 22 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd) | |
| ---> 23 _do_run(cmd, checks, log_stdout, env=env) | |
| cmd = 'unset R_HOME && unset R_LIBS && export PATH=/mnt..._analysis/work/mutect2/1-effects-annotated.vcf.gz' | |
| checks = None | |
| log_stdout = False | |
| env = None | |
| 24 except: | |
| 25 diagnostics.end_cmd(cmd_id, False) | |
| 26 if log_error: | |
| 27 logger.exception() | |
| ........................................................................... | |
| /home/mbeyens/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py in _do_run(cmd='set -o pipefail; unset R_HOME && unset R_LIBS &&..._analysis/work/mutect2/1-effects-annotated.vcf.gz', checks=None, log_stdout=False, env=None) | |
| 98 error_msg = " ".join(cmd) if not isinstance(cmd, basestring) else cmd | |
| 99 error_msg += "\n" | |
| 100 error_msg += "".join(debug_stdout) | |
| 101 s.communicate() | |
| 102 s.stdout.close() | |
| --> 103 raise subprocess.CalledProcessError(exitcode, error_msg) | |
| exitcode = 139 | |
| error_msg = 'set -o pipefail; unset R_HOME && unset R_LIBS &&...analysis/work/mutect2/1-effects-annotated.vcf.gz\n' | |
| 104 else: | |
| 105 break | |
| 106 s.communicate() | |
| 107 s.stdout.close() | |
| CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin:$PATH && export TMPDIR=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7 && /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| Selected test sample P00132893_tumor and control sample P00132893_normal | |
| /bin/bash: line 1: 65589 Segmentation fault (core dumped) /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| ' returned non-zero exit status 139 | |
| ___________________________________________________________________________ | |
| 22 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd) | |
| ---> 23 _do_run(cmd, checks, log_stdout, env=env) | |
| cmd = 'unset R_HOME && unset R_LIBS && export PATH=/mnt..._analysis/work/mutect2/1-effects-annotated.vcf.gz' | |
| checks = None | |
| log_stdout = False | |
| env = None | |
| 24 except: | |
| 25 diagnostics.end_cmd(cmd_id, False) | |
| 26 if log_error: | |
| 27 logger.exception() | |
| ........................................................................... | |
| /home/mbeyens/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py in _do_run(cmd='set -o pipefail; unset R_HOME && unset R_LIBS &&..._analysis/work/mutect2/1-effects-annotated.vcf.gz', checks=None, log_stdout=False, env=None) | |
| 98 error_msg = " ".join(cmd) if not isinstance(cmd, basestring) else cmd | |
| 99 error_msg += "\n" | |
| 100 error_msg += "".join(debug_stdout) | |
| 101 s.communicate() | |
| 102 s.stdout.close() | |
| --> 103 raise subprocess.CalledProcessError(exitcode, error_msg) | |
| exitcode = 139 | |
| error_msg = 'set -o pipefail; unset R_HOME && unset R_LIBS &&...analysis/work/mutect2/1-effects-annotated.vcf.gz\n' | |
| 104 else: | |
| 105 break | |
| 106 s.communicate() | |
| 107 s.stdout.close() | |
| CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin:$PATH && export TMPDIR=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7 && /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| Selected test sample P00132893_tumor and control sample P00132893_normal | |
| /bin/bash: line 1: 65589 Segmentation fault (core dumped) /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| ' returned non-zero exit status 139 | |
| ___________________________________________________________________________ | |
| mbeyens@trainingvm-n001:/home/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work$ | |
| 282 | |
| 283 def _cnvkit_metrics(cnns, target_bed, antitarget_bed, cov_interval, items): | |
| 284 """Estimate noise of a sample using a flat background. | |
| ........................................................................... | |
| /home/mbeyens/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py in run(cmd='unset R_HOME && unset R_LIBS && export PATH=/mnt..._analysis/work/mutect2/1-effects-annotated.vcf.gz', descr='CNVkit segment', data=None, checks=None, region=None, log_error=True, log_stdout=False, env=None) | |
| 18 descr = _descr_str(descr, data, region) | |
| 19 logger.debug(descr) | |
| 20 cmd_id = diagnostics.start_cmd(cmd, descr or "", data) | |
| 21 try: | |
| 22 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd) | |
| ---> 23 _do_run(cmd, checks, log_stdout, env=env) | |
| cmd = 'unset R_HOME && unset R_LIBS && export PATH=/mnt..._analysis/work/mutect2/1-effects-annotated.vcf.gz' | |
| checks = None | |
| log_stdout = False | |
| env = None | |
| 24 except: | |
| 25 diagnostics.end_cmd(cmd_id, False) | |
| 26 if log_error: | |
| 27 logger.exception() | |
| ........................................................................... | |
| /home/mbeyens/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py in _do_run(cmd='set -o pipefail; unset R_HOME && unset R_LIBS &&..._analysis/work/mutect2/1-effects-annotated.vcf.gz', checks=None, log_stdout=False, env=None) | |
| 98 error_msg = " ".join(cmd) if not isinstance(cmd, basestring) else cmd | |
| 99 error_msg += "\n" | |
| 100 error_msg += "".join(debug_stdout) | |
| 101 s.communicate() | |
| 102 s.stdout.close() | |
| --> 103 raise subprocess.CalledProcessError(exitcode, error_msg) | |
| exitcode = 139 | |
| error_msg = 'set -o pipefail; unset R_HOME && unset R_LIBS &&...analysis/work/mutect2/1-effects-annotated.vcf.gz\n' | |
| 104 else: | |
| 105 break | |
| 106 s.communicate() | |
| 107 s.stdout.close() | |
| CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin:$PATH && export TMPDIR=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7 && /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| Selected test sample P00132893_tumor and control sample P00132893_normal | |
| /bin/bash: line 1: 65589 Segmentation fault (core dumped) /mnt/home_nfs1/mbeyens/local/share/bcbio/anaconda/bin/cnvkit.py segment -p 16 -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpx6HuN7/P00132893_tumor-sort-1.cns /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/structural/P00132893_tumor/cnvkit/raw/P00132893_tumor-sort-1.cnr -v /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-annotated.vcf.gz | |
| ' returned non-zero exit status 139 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment