.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS (1029_0I)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/4bde57b27673ee894fc2d64d872961/.command.log
Size: 11.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS (1029_0I)
Attempt
Content

  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/4bde57b27673ee894fc2d64d872961/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0I-N1-BDNA-1_B23KGCJLT4_1/1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0I-T1-TDNA-1_A23KCGYLT4_1/1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/4bde57b27673ee894fc2d64d872961/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0I-N1-BDNA-1_B23KGCJLT4_1/1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0I-T1-TDNA-1_A23KCGYLT4_1/1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 302.357764 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 210.050977 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 178.230558 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 84.122399 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 91.168521 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 154.267172 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 177.069009 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 95.218334 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 117.301947 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 77.542434 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 109.922067 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 160.780830 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 55.974724 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 54.921587 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 150.091021 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 121.014881 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 130.672368 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 42.141796 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 123.624351 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 62.082011 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 25.879476 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 89.767068 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 61.652244 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 2.144935 seconds.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Finished in 0.452498 seconds.