.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM (1136_6I8-N1-BDNA-1_B23MHTGLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/67dd9630dcc2847c3db463f0142d59/.command.log
Size: 1.1 KB
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM (1136_6I8-N1-BDNA-1_B23MHTGLT4_1)
Attempt

Content

  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/12/0c4c75d2da3fb6261e3b47f7f8c252/1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq_tumor_only.filtered_snpEff.ann.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/67dd9630dcc2847c3db463f0142d59/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/67dd9630dcc2847c3db463f0142d59/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/0c4c75d2da3fb6261e3b47f7f8c252/1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq_tumor_only.filtered_snpEff.ann.vcf.gz.tbi
==> STAGING COMPLETE (5 inputs)

Lines   total/split/joined/realigned/mismatch_removed/dup_removed/skipped:	18385/3156/0/6119/0/0/0
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