.command.log - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS (HCC1395_BL)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/37734258db05eeea95ce281ae4c6d8/.command.log
Size: 2.2 KB
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS (HCC1395_BL)
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/e6/37734258db05eeea95ce281ae4c6d8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/37734258db05eeea95ce281ae4c6d8/.command.run
  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_BL/HCC1395_BL.recalibrated.bam
ERROR "ls s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam": no object found
ERROR "cp s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam HCC1395_BL.recalibrated.bam": NoSuchKey: The specified key does not exist. status code: 404, request id: VARKGXBFDBDXS3Z6, host id: wco5CASuppsh1TrqacJfNpGNhdB3ZcSRHxf0ZMSUszYDPrpVstrchqgPyKpq0KBdD8ZZqm3TyBc=
  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_BL/HCC1395_BL.recalibrated.bam.bai
ERROR "ls s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai": no object found
ERROR "cp s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai HCC1395_BL.recalibrated.bam.bai": NoSuchKey: The specified key does not exist. status code: 404, request id: ATNF98HE7N0EKV7H, host id: Ahpi+EmaK/K1W/YxL4e6Q3quc2nriSS5ysdJwjt2o9700NsW4oiRUS5sILXaoXpLosHG2LYHETk=