.command.log - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP (HCC1395_tumor;SNP_GRCh38_hg38_wChr)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/63e5c78668302e26d64b47d81db841/.command.log
Size: 967 bytes
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP (HCC1395_tumor;SNP_GRCh38_hg38_wChr)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/63e5c78668302e26d64b47d81db841/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/63e5c78668302e26d64b47d81db841/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
==> STAGING COMPLETE (5 inputs)

[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
ls: *.mpileup.gz: No such file or directory