.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM (869_XTN-N1-BDNA-1_A23FG3YLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/0cb38c655feb923a8328696b27727d/.command.log
Size: 1.1 KB
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM (869_XTN-N1-BDNA-1_A23FG3YLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/5e164398dafbda2de767d0a44677b8/869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.filtered_snpEff.ann.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/0cb38c655feb923a8328696b27727d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/0cb38c655feb923a8328696b27727d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/5e164398dafbda2de767d0a44677b8/869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.filtered_snpEff.ann.vcf.gz
==> STAGING COMPLETE (5 inputs)

Lines   total/split/joined/realigned/mismatch_removed/dup_removed/skipped:	18978/3834/0/6852/0/0/0
ls: cannot access '*.vcf': No such file or directory
ls: cannot access '*.bcf': No such file or directory
ls: cannot access '*.bcf.gz': No such file or directory
ls: cannot access '*.csi': No such file or directory