.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS (1029_11H)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/b17fd3e13fe81ef108601505648ca7/.command.log
Size: 10.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS (1029_11H)
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/e8/b17fd3e13fe81ef108601505648ca7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_11H-N1-BDNA-1_B23KGCJLT4_1/1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/b17fd3e13fe81ef108601505648ca7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_11H-N1-BDNA-1_B23KGCJLT4_1/1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
  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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 245.174734 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 191.791820 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 190.716816 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 112.091699 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 115.014443 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 160.524164 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 187.425513 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 105.851793 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 142.570504 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 110.087096 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 127.587365 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 157.892239 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 48.573916 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 111.588981 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 101.572686 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 98.520137 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 209.183993 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 45.656568 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 135.236511 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 52.407752 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 26.291562 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_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai