.command.log - Workdir - MUTECT2_TUMOR_ONLY (LS0879)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/f5/d6c27c4fea6dcdea8bc01625232d86/.command.log
Size: 1.6 KB
Task: MUTECT2_TUMOR_ONLY (LS0879)
Attempt

Content

  Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0879/LS0879_tumor.bam
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/f5/d6c27c4fea6dcdea8bc01625232d86/.command.sh
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/TSO500/TST500C_manifest.bed/TST500C_manifest.bed
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz
ERROR "ls s3://fsdx-algo-644019535899-us-west-2-an/TSO500/TST500C_manifest.bed/TST500C_manifest.bed": no object found
ERROR "cp s3://fsdx-algo-644019535899-us-west-2-an/TSO500/TST500C_manifest.bed/TST500C_manifest.bed TST500C_manifest.bed": NoSuchKey: The specified key does not exist. status code: 404, request id: KD23VS3YG40BTHCD, host id: L0Drlo9zxufwz57h8Ok6YKYhGQeQ5mp7fIYnCuGc8X32LFL4X1ZEjVaLYEF12hEgMQpzvUZKR1PBHBzVEr1MzrLZQzqWrO+h
ERROR "cp s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa hg38.fa": rename ./hg38.fa2482459498 hg38.fa: no such file or directory
ERROR "cp s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz af-only-gnomad.hg38.vcf.gz": rename ./af-only-gnomad.hg38.vcf.gz385156352 af-only-gnomad.hg38.vcf.gz: no such file or directory
ERROR "cp s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0879/LS0879_tumor.bam LS0879_tumor.bam": rename ./LS0879_tumor.bam1836198478 LS0879_tumor.bam: no such file or directory