.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (1029_0W2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/330fd8e17ba545cec2238bb0786478/.command.log
Size: 867 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (1029_0W2)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/330fd8e17ba545cec2238bb0786478/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/d1ed11159c4c263c32919ba8b8e827/1029_0W2.purity_ploidy.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/330fd8e17ba545cec2238bb0786478/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/d1ed11159c4c263c32919ba8b8e827/1029_0W2.segments.csv
==> STAGING COMPLETE (4 inputs)

Determining HRD-LOH, LST, TAI 
scarHRD input saved for 1029_0W2
building scarHRD command
Rscript -e 'library(data.table);library(scarHRD);df <- scar_score("./1029_0W2.scarHRD.input.txt", reference = "grch38", seqz=FALSE);dimnames(df) <- list(NULL, c("LOH","TAI","LST","HRD_score"));fwrite(as.data.table(df), "./1029_0W2.scarHRD.output.score.csv")'
Running scarHRD