.command.log - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:CRAM_HLATYPING_ALL:CRAM_FILTER_HLA (germline_control_4)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/e4b7d81d5650a67b6a2ec33afef81d/.command.log
Size: 1.3 KB
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:CRAM_HLATYPING_ALL:CRAM_FILTER_HLA (germline_control_4)
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/31/fa5be6df9c564f4abfff8ac00295cf/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/fa5be6df9c564f4abfff8ac00295cf/NA12878_c_0002_gDNA_0004_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/e4b7d81d5650a67b6a2ec33afef81d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/e4b7d81d5650a67b6a2ec33afef81d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (6 inputs)


sambamba 1.0.1
 by Artem Tarasov and Pjotr Prins (C) 2012-2023
    LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0)


sambamba 1.0.1
 by Artem Tarasov and Pjotr Prins (C) 2012-2023
    LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0)

[M::bam2fq_mainloop] discarded 9108 singletons
[M::bam2fq_mainloop] processed 2675154 reads