.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS (1029_01S)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/d979108a736de9039bc83fca8fbf20/.command.log
Size: 7.8 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS (1029_01S)
Attempt
Content

  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_01S-N1-BDNA-1_B23KGCJLT4_1/1029_01S-N1-BDNA-1_B23KGCJLT4_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.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/d979108a736de9039bc83fca8fbf20/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_01S-N1-BDNA-1_B23KGCJLT4_1/1029_01S-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_01S-T1-TDNA-1_B23KFCWLT4_1/1029_01S-T1-TDNA-1_B23KFCWLT4_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_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_01S-T1-TDNA-1_B23KFCWLT4_1/1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/d979108a736de9039bc83fca8fbf20/.command.run
  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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 324.832831 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 283.245891 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 226.136099 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 139.210585 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 157.214804 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 231.700602 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 220.381487 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 180.677970 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 187.020622 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 128.470187 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 164.815701 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 218.574334 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Finished in 65.452180 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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai