Open WuRAFY opened 1 year ago
Version info
bcbio_nextgen.py --version
lsb_release -ds
To Reproduce Exact bcbio command you have used:
bcbio_nextgen.py ../config/pon.yaml -n 15
Your yaml configuration file:
details: - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM01_10 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM01_10_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM02_20 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM02_20_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM03_14 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM03_14_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM05_13 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM05_13_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM06_29 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM06_29_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM07_11 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM07_11_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM08_13 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM08_13_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM09_08 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM09_08_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM10_14 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM10_14_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM11_11 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM11_11_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM12_13 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM12_13_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM14_12 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM14_12_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM15_12 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM15_12_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal - algorithm: aligner: false svcaller: purecn variant_regions: /project/wufy/LUAD/workdir/bcbio/S07604514_gene_Padded_merged.bed variantcaller: mutect2 analysis: variant2 description: LUAD_RM16_11 files: - /project/wufy/LUAD/workdir/bcbio/pon/input/LUAD_RM16_11_sort_MD_BQSR.bam genome_build: hg38 metadata: batch: pon_build phenotype: normal fc_name: pon upload: dir: ../final
Log files (could be found in work/log)
[2023-06-03T11:31Z] System YAML configuration: /project/wufy2/bcbio/galaxy/bcbio_system.yaml. [2023-06-03T11:31Z] Locale set to en_US.utf8. [2023-06-03T11:31Z] Resource requests: sambamba, samtools; memory: 4.00, 4.00; cores: 16, 16 [2023-06-03T11:31Z] Configuring 1 jobs to run, using 15 cores each with 60.1g of memory reserved for each job [2023-06-03T11:31Z] Timing: organize samples [2023-06-03T11:31Z] multiprocessing: organize_samples [2023-06-03T11:31Z] Using input YAML configuration: /project/wufy/LUAD/workdir/bcbio/pon/config/pon.yaml [2023-06-03T11:31Z] Checking sample YAML configuration: /project/wufy/LUAD/workdir/bcbio/pon/config/pon.yaml [2023-06-03T11:31Z] Retreiving program versions from /project/wufy2/bcbio/manifest/python-packages.yaml. [2023-06-03T11:31Z] Retreiving program versions from /project/wufy2/bcbio/manifest/r-packages.yaml. [2023-06-03T11:31Z] Testing minimum versions of installed programs [2023-06-03T11:31Z] Timing: alignment preparation [2023-06-03T11:31Z] multiprocessing: prep_align_inputs [2023-06-03T11:31Z] multiprocessing: disambiguate_split [2023-06-03T11:31Z] Timing: alignment [2023-06-03T11:31Z] multiprocessing: process_alignment [2023-06-03T11:32Z] Timing: callable regions [2023-06-03T11:32Z] multiprocessing: prep_samples [2023-06-03T11:32Z] multiprocessing: postprocess_alignment [2023-06-03T11:32Z] LUAD_RM01_10: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM02_20: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM03_14: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM05_13: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM06_29: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM07_11: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM08_13: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM09_08: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM10_14: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM11_11: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM12_13: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM14_12: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM15_12: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] LUAD_RM16_11: Assigned coverage as 'amplicon' with 3.1% genome coverage and -0.1% offtarget coverage [2023-06-03T11:32Z] multiprocessing: combine_sample_regions [2023-06-03T11:32Z] Identified 196 parallel analysis blocks Block sizes: min: 756249 5%: 6820211.25 25%: 16090731.25 median: 16126655.0 75%: 16300911.25 95%: 18551059.5 99%: 28537205.450000007 max: 37925193 Between block sizes: min: 287 5%: 440.2 25%: 1728.5 median: 7670.5 75%: 31434.5 95%: 369338.4499999976 99%: 1192666.5999999973 max: 3319465 [2023-06-03T11:32Z] multiprocessing: calculate_sv_bins [2023-06-03T11:32Z] multiprocessing: calculate_sv_coverage [2023-06-03T11:32Z] multiprocessing: normalize_sv_coverage [2023-06-03T11:32Z] Timing: hla typing [2023-06-03T11:32Z] Resource requests: gatk, mutect2, picard; memory: 4.00, 4.00, 4.00; cores: 16, 16, 16 [2023-06-03T11:32Z] Configuring 15 jobs to run, using 1 cores each with 4.00g of memory reserved for each job [2023-06-03T11:32Z] Timing: alignment post-processing [2023-06-03T11:32Z] multiprocessing: piped_bamprep [2023-06-03T11:32Z] Timing: variant calling [2023-06-03T11:32Z] multiprocessing: variantcall_sample [2023-06-03T11:32Z] multiprocessing: concat_variant_files [2023-06-03T11:32Z] Timing: joint squaring off/backfilling [2023-06-03T11:32Z] Resource requests: bcbio_variation, fastqc, gatk, gemini, kraken, preseq, purecn, qsignature, sambamba, samtools, snpeff; memory: 4.00, 4.00, 4.00, 4.00, 4.00, 4.00, 4.00, 4.00, 4.00, 4.00, 3.00; cores: 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1 [2023-06-03T11:32Z] Configuring 1 jobs to run, using 15 cores each with 60.1g of memory reserved for each job [2023-06-03T11:32Z] Timing: variant post-processing [2023-06-03T11:32Z] multiprocessing: postprocess_variants [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM01_10, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM01_10, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM01_10, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM01_10, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM01_10, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM02_20, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM02_20, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM02_20, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM02_20, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM02_20, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM03_14, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM03_14, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM03_14, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM03_14, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM03_14, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM05_13, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM05_13, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM05_13, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM05_13, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM05_13, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM06_29, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM06_29, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM06_29, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM06_29, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM06_29, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM07_11, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM07_11, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM07_11, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM07_11, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM07_11, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM08_13, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM08_13, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM08_13, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM08_13, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM08_13, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM09_08, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM09_08, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM09_08, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM09_08, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM09_08, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM10_14, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM10_14, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM10_14, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM10_14, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM10_14, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM11_11, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM11_11, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM11_11, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM11_11, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM11_11, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM12_13, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM12_13, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM12_13, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM12_13, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM12_13, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM14_12, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM14_12, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM14_12, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM14_12, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM14_12, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM15_12, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM15_12, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM15_12, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM15_12, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM15_12, mutect2 [2023-06-03T11:32Z] Finalizing variant calls: LUAD_RM16_11, mutect2 [2023-06-03T11:32Z] Calculating variation effects for LUAD_RM16_11, mutect2 [2023-06-03T11:32Z] Annotate VCF file: LUAD_RM16_11, mutect2 [2023-06-03T11:32Z] Filtering for LUAD_RM16_11, mutect2 [2023-06-03T11:32Z] Prioritization for LUAD_RM16_11, mutect2 [2023-06-03T11:32Z] multiprocessing: split_variants_by_sample [2023-06-03T11:32Z] Timing: prepped BAM merging [2023-06-03T11:32Z] Timing: validation [2023-06-03T11:32Z] multiprocessing: compare_to_rm [2023-06-03T11:32Z] Timing: ensemble calling [2023-06-03T11:32Z] Timing: validation summary [2023-06-03T11:32Z] Timing: structural variation [2023-06-03T11:32Z] Timing: structural variation [2023-06-03T11:32Z] Timing: structural variation ensemble [2023-06-03T11:32Z] Timing: structural variation validation [2023-06-03T11:32Z] multiprocessing: validate_sv [2023-06-03T11:32Z] Timing: heterogeneity [2023-06-03T11:32Z] Timing: population database [2023-06-03T11:32Z] multiprocessing: prep_gemini_db [2023-06-03T11:32Z] Not running gemini, no samples with variants found: LUAD_RM01_10, LUAD_RM02_20, LUAD_RM03_14, LUAD_RM05_13, LUAD_RM06_29, LUAD_RM07_11, LUAD_RM08_13, LUAD_RM09_08, LUAD_RM10_14, LUAD_RM11_11, LUAD_RM12_13, LUAD_RM14_12, LUAD_RM15_12, LUAD_RM16_11 [2023-06-03T11:32Z] Timing: create CNV PON [2023-06-03T11:32Z] PureCN normalDB [2023-06-03T11:32Z] Warning message: [2023-06-03T11:32Z] package ‘optparse’ was built under R version 4.1.3 [2023-06-03T11:32Z] Warning message: [2023-06-03T11:32Z] package ‘futile.logger’ was built under R version 4.1.3 [2023-06-03T11:32Z] INFO [2023-06-03 19:32:28] Loading PureCN 2.0.2... [2023-06-03T11:32Z] INFO [2023-06-03 19:32:29] Creating mapping bias database. [2023-06-03T11:32Z] INFO [2023-06-03 19:32:30] Processing variants 1 to 50000... [2023-06-03T11:32Z] INFO [2023-06-03 19:32:47] Clustering beta binomial fits... [2023-06-03T11:32Z] INFO [2023-06-03 19:32:50] Assigning (600/1556) variants a clustered beta binomal fit. [2023-06-03T11:32Z] WARN [2023-06-03 19:32:51] Found 1556.000000 variants in mapping bias database. [2023-06-03T11:32Z] There were 13 warnings (use warnings() to see them) [2023-06-03T11:32Z] INFO [2023-06-03 19:32:51] Creating normalDB... [2023-06-03T11:34Z] Error in (function (fmt, ...) : [2023-06-03T11:34Z] invalid format '%i'; use format %f, %e, %g or %a for numeric objects [2023-06-03T11:34Z] Calls: createNormalDatabase ... flog.info -> .log_level -> layout -> do.call -> <Anonymous> [2023-06-03T11:34Z] Execution halted [2023-06-03T11:34Z] Uncaught exception occurred Traceback (most recent call last): File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/provenance/do.py", line 26, in run _do_run(cmd, checks, log_stdout, env=env) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/provenance/do.py", line 106, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) subprocess.CalledProcessError: Command 'set -o pipefail; export R_LIBS_USER=/project/wufy2/bcbio/anaconda/lib/R/library && unset R_HOME && unset R_LIBS && export PATH=/project/wufy2/bcbio/anaconda/bin:"$PATH" && /project/wufy2/bcbio/anaconda/bin/Rscript /project/wufy2/bcbio/anaconda/lib/R/library/PureCN/extdata/NormalDB.R --out-dir /project/wufy/LUAD/workdir/bcbio/pon/work/gemini --coverage-files /project/wufy/LUAD/workdir/bcbio/pon/work/gemini/purecn_coverage_files.txt --normal-panel /project/wufy/LUAD/workdir/bcbio/pon/work/gemini/pon_build-mutect2.vcf.gz --genome hg38 --force Warning message: package ‘optparse’ was built under R version 4.1.3 Warning message: package ‘futile.logger’ was built under R version 4.1.3 INFO [2023-06-03 19:32:28] Loading PureCN 2.0.2... INFO [2023-06-03 19:32:29] Creating mapping bias database. INFO [2023-06-03 19:32:30] Processing variants 1 to 50000... INFO [2023-06-03 19:32:47] Clustering beta binomial fits... INFO [2023-06-03 19:32:50] Assigning (600/1556) variants a clustered beta binomal fit. WARN [2023-06-03 19:32:51] Found 1556.000000 variants in mapping bias database. There were 13 warnings (use warnings() to see them) INFO [2023-06-03 19:32:51] Creating normalDB... Error in (function (fmt, ...) : invalid format '%i'; use format %f, %e, %g or %a for numeric objects Calls: createNormalDatabase ... flog.info -> .log_level -> layout -> do.call -> <Anonymous> Execution halted ' returned non-zero exit status 1. [2023-06-03T11:34Z] PureCN failed to create a normal db [2023-06-03T11:34Z] Timing: peddy check [2023-06-03T11:34Z] multiprocessing: run_peddy [2023-06-03T11:34Z] Timing: quality control [2023-06-03T11:34Z] multiprocessing: pipeline_summary [2023-06-03T11:34Z] QC: LUAD_RM01_10 contamination [2023-06-03T11:34Z] QC: LUAD_RM01_10 coverage [2023-06-03T11:34Z] QC: LUAD_RM01_10 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM01_10/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM01_10 peddy [2023-06-03T11:34Z] QC: LUAD_RM01_10 picard [2023-06-03T11:34Z] QC: LUAD_RM01_10 qsignature [2023-06-03T11:34Z] QC: LUAD_RM01_10 samtools [2023-06-03T11:34Z] QC: LUAD_RM01_10 variants [2023-06-03T11:34Z] QC: LUAD_RM01_10 viral [2023-06-03T11:34Z] QC: LUAD_RM02_20 contamination [2023-06-03T11:34Z] QC: LUAD_RM02_20 coverage [2023-06-03T11:34Z] QC: LUAD_RM02_20 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM02_20/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM02_20 peddy [2023-06-03T11:34Z] QC: LUAD_RM02_20 picard [2023-06-03T11:34Z] QC: LUAD_RM02_20 qsignature [2023-06-03T11:34Z] QC: LUAD_RM02_20 samtools [2023-06-03T11:34Z] QC: LUAD_RM02_20 variants [2023-06-03T11:34Z] QC: LUAD_RM02_20 viral [2023-06-03T11:34Z] QC: LUAD_RM03_14 contamination [2023-06-03T11:34Z] QC: LUAD_RM03_14 coverage [2023-06-03T11:34Z] QC: LUAD_RM03_14 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM03_14/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM03_14 peddy [2023-06-03T11:34Z] QC: LUAD_RM03_14 picard [2023-06-03T11:34Z] QC: LUAD_RM03_14 qsignature [2023-06-03T11:34Z] QC: LUAD_RM03_14 samtools [2023-06-03T11:34Z] QC: LUAD_RM03_14 variants [2023-06-03T11:34Z] QC: LUAD_RM03_14 viral [2023-06-03T11:34Z] QC: LUAD_RM05_13 contamination [2023-06-03T11:34Z] QC: LUAD_RM05_13 coverage [2023-06-03T11:34Z] QC: LUAD_RM05_13 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM05_13/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM05_13 peddy [2023-06-03T11:34Z] QC: LUAD_RM05_13 picard [2023-06-03T11:34Z] QC: LUAD_RM05_13 qsignature [2023-06-03T11:34Z] QC: LUAD_RM05_13 samtools [2023-06-03T11:34Z] QC: LUAD_RM05_13 variants [2023-06-03T11:34Z] QC: LUAD_RM05_13 viral [2023-06-03T11:34Z] QC: LUAD_RM06_29 contamination [2023-06-03T11:34Z] QC: LUAD_RM06_29 coverage [2023-06-03T11:34Z] QC: LUAD_RM06_29 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM06_29/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM06_29 peddy [2023-06-03T11:34Z] QC: LUAD_RM06_29 picard [2023-06-03T11:34Z] QC: LUAD_RM06_29 qsignature [2023-06-03T11:34Z] QC: LUAD_RM06_29 samtools [2023-06-03T11:34Z] QC: LUAD_RM06_29 variants [2023-06-03T11:34Z] QC: LUAD_RM06_29 viral [2023-06-03T11:34Z] QC: LUAD_RM07_11 contamination [2023-06-03T11:34Z] QC: LUAD_RM07_11 coverage [2023-06-03T11:34Z] QC: LUAD_RM07_11 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM07_11/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM07_11 peddy [2023-06-03T11:34Z] QC: LUAD_RM07_11 picard [2023-06-03T11:34Z] QC: LUAD_RM07_11 qsignature [2023-06-03T11:34Z] QC: LUAD_RM07_11 samtools [2023-06-03T11:34Z] QC: LUAD_RM07_11 variants [2023-06-03T11:34Z] QC: LUAD_RM07_11 viral [2023-06-03T11:34Z] QC: LUAD_RM08_13 contamination [2023-06-03T11:34Z] QC: LUAD_RM08_13 coverage [2023-06-03T11:34Z] QC: LUAD_RM08_13 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM08_13/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM08_13 peddy [2023-06-03T11:34Z] QC: LUAD_RM08_13 picard [2023-06-03T11:34Z] QC: LUAD_RM08_13 qsignature [2023-06-03T11:34Z] QC: LUAD_RM08_13 samtools [2023-06-03T11:34Z] QC: LUAD_RM08_13 variants [2023-06-03T11:34Z] QC: LUAD_RM08_13 viral [2023-06-03T11:34Z] QC: LUAD_RM09_08 contamination [2023-06-03T11:34Z] QC: LUAD_RM09_08 coverage [2023-06-03T11:34Z] QC: LUAD_RM09_08 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM09_08/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM09_08 peddy [2023-06-03T11:34Z] QC: LUAD_RM09_08 picard [2023-06-03T11:34Z] QC: LUAD_RM09_08 qsignature [2023-06-03T11:34Z] QC: LUAD_RM09_08 samtools [2023-06-03T11:34Z] QC: LUAD_RM09_08 variants [2023-06-03T11:34Z] QC: LUAD_RM09_08 viral [2023-06-03T11:34Z] QC: LUAD_RM10_14 contamination [2023-06-03T11:34Z] QC: LUAD_RM10_14 coverage [2023-06-03T11:34Z] QC: LUAD_RM10_14 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM10_14/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM10_14 peddy [2023-06-03T11:34Z] QC: LUAD_RM10_14 picard [2023-06-03T11:34Z] QC: LUAD_RM10_14 qsignature [2023-06-03T11:34Z] QC: LUAD_RM10_14 samtools [2023-06-03T11:34Z] QC: LUAD_RM10_14 variants [2023-06-03T11:34Z] QC: LUAD_RM10_14 viral [2023-06-03T11:34Z] QC: LUAD_RM11_11 contamination [2023-06-03T11:34Z] QC: LUAD_RM11_11 coverage [2023-06-03T11:34Z] QC: LUAD_RM11_11 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM11_11/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM11_11 peddy [2023-06-03T11:34Z] QC: LUAD_RM11_11 picard [2023-06-03T11:34Z] QC: LUAD_RM11_11 qsignature [2023-06-03T11:34Z] QC: LUAD_RM11_11 samtools [2023-06-03T11:34Z] QC: LUAD_RM11_11 variants [2023-06-03T11:34Z] QC: LUAD_RM11_11 viral [2023-06-03T11:34Z] QC: LUAD_RM12_13 contamination [2023-06-03T11:34Z] QC: LUAD_RM12_13 coverage [2023-06-03T11:34Z] QC: LUAD_RM12_13 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM12_13/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM12_13 peddy [2023-06-03T11:34Z] QC: LUAD_RM12_13 picard [2023-06-03T11:34Z] QC: LUAD_RM12_13 qsignature [2023-06-03T11:34Z] QC: LUAD_RM12_13 samtools [2023-06-03T11:34Z] QC: LUAD_RM12_13 variants [2023-06-03T11:34Z] QC: LUAD_RM12_13 viral [2023-06-03T11:34Z] QC: LUAD_RM14_12 contamination [2023-06-03T11:34Z] QC: LUAD_RM14_12 coverage [2023-06-03T11:34Z] QC: LUAD_RM14_12 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM14_12/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM14_12 peddy [2023-06-03T11:34Z] QC: LUAD_RM14_12 picard [2023-06-03T11:34Z] QC: LUAD_RM14_12 qsignature [2023-06-03T11:34Z] QC: LUAD_RM14_12 samtools [2023-06-03T11:34Z] QC: LUAD_RM14_12 variants [2023-06-03T11:34Z] QC: LUAD_RM14_12 viral [2023-06-03T11:34Z] QC: LUAD_RM15_12 contamination [2023-06-03T11:34Z] QC: LUAD_RM15_12 coverage [2023-06-03T11:34Z] QC: LUAD_RM15_12 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM15_12/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM15_12 peddy [2023-06-03T11:34Z] QC: LUAD_RM15_12 picard [2023-06-03T11:34Z] QC: LUAD_RM15_12 qsignature [2023-06-03T11:34Z] QC: LUAD_RM15_12 samtools [2023-06-03T11:34Z] QC: LUAD_RM15_12 variants [2023-06-03T11:34Z] QC: LUAD_RM15_12 viral [2023-06-03T11:34Z] QC: LUAD_RM16_11 contamination [2023-06-03T11:34Z] QC: LUAD_RM16_11 coverage [2023-06-03T11:34Z] QC: LUAD_RM16_11 fastqc [2023-06-03T11:34Z] Produced HTML report /project/wufy/LUAD/workdir/bcbio/pon/work/qc/LUAD_RM16_11/fastqc/fastqc_report.html [2023-06-03T11:34Z] QC: LUAD_RM16_11 peddy [2023-06-03T11:34Z] QC: LUAD_RM16_11 picard [2023-06-03T11:34Z] QC: LUAD_RM16_11 qsignature [2023-06-03T11:34Z] QC: LUAD_RM16_11 samtools [2023-06-03T11:34Z] QC: LUAD_RM16_11 variants [2023-06-03T11:34Z] QC: LUAD_RM16_11 viral [2023-06-03T11:34Z] multiprocessing: qsignature_summary [2023-06-03T11:34Z] summarize metadata [2023-06-03T11:34Z] multiprocessing: multiqc_summary [2023-06-03T11:34Z] summarize target information [2023-06-03T11:34Z] summarize fastqc Traceback (most recent call last): File "/project/wufy2/bcbio/tools/bin/bcbio_nextgen.py", line 245, in <module> main(**kwargs) File "/project/wufy2/bcbio/tools/bin/bcbio_nextgen.py", line 46, in main run_main(**kwargs) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 50, in run_main fc_dir, run_info_yaml) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel for xs in pipeline(config, run_info_yaml, parallel, dirs, samples): File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 194, in variant2pipeline samples = qcsummary.generate_parallel(samples, run_parallel) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/qcsummary.py", line 59, in generate_parallel return [[utils.to_single_data(d)] for d in run_parallel("multiqc_summary", [out])] File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel return run_multicore(fn, items, config, parallel=parallel) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items): File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 1048, in __call__ if self.dispatch_one_batch(iterator): File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 866, in dispatch_one_batch self._dispatch(tasks) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 784, in _dispatch job = self._backend.apply_async(batch, callback=cb) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 208, in apply_async result = ImmediateResult(func) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 572, in __init__ self.results = batch() File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 263, in __call__ for func, args, kwargs in self.items] File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 263, in <listcomp> for func, args, kwargs in self.items] File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/utils.py", line 59, in wrapper return f(*args, **kwargs) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/multitasks.py", line 255, in multiqc_summary return multiqc.summary(*args) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/qc/multiqc.py", line 88, in summary data_json_final = _save_uploaded_data_json(samples, data_json, os.path.join(out_dir, "multiqc_data")) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/qc/multiqc.py", line 146, in _save_uploaded_data_json upload_path_mapping.update(get_all_upload_paths_from_sample(sample)) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/upload/__init__.py", line 46, in get_all_upload_paths_from_sample for finfo in _get_files_project(sample, upload_config): File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/upload/__init__.py", line 963, in _get_files_project return _add_meta(out, config=upload_config) File "/project/wufy2/bcbio/anaconda/lib/python3.7/site-packages/bcbio/upload/__init__.py", line 161, in _add_meta raise ValueError("Unexpected path for upload: %s" % x) ValueError: Unexpected path for upload: {'path': '/project/wufy/LUAD/workdir/bcbio/pon/work/gemini/normalDB_hg38.rds'}
Version info
bcbio_nextgen.py --version):1.2.9lsb_release -ds):CentOS Linux release 7.5.1804 (Core)To Reproduce Exact bcbio command you have used:
Your yaml configuration file:
Log files (could be found in work/log)