.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_GERMLINE:BCFTOOLS_NORM (1136_7L-N1-BDNA-1_A237CFYLT3_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/2ba8b32565e93e40f47f49ddf49270/.command.log
Size: 1.0 KB
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_GERMLINE:BCFTOOLS_NORM (1136_7L-N1-BDNA-1_A237CFYLT3_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/4c/5c3e584a9c1a54ce66e8892c4d2ce1/1136_7L-N1-BDNA-1_A237CFYLT3_1.haplotyper_rf.gt_corrected.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/2ba8b32565e93e40f47f49ddf49270/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/2ba8b32565e93e40f47f49ddf49270/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/65a02f26c3e06b3441e7ba1f74d974/1136_7L-N1-BDNA-1_A237CFYLT3_1.haplotyper_rf.gt_corrected.vcf.gz
==> STAGING COMPLETE (5 inputs)

Lines   total/split/joined/realigned/mismatch_removed/dup_removed/skipped:	30329/0/0/0/0/0/0
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