.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (custom_Sig_18_tumor_normal)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/c6bc34ed5de5a47a33922742bc3424/.command.log
Size: 957 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (custom_Sig_18_tumor_normal)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/b73023e395d194b78be262456e6141/custom_Sig_18_tumor_normal.segments.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/b73023e395d194b78be262456e6141/custom_Sig_18_tumor_normal.purity_ploidy.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/c6bc34ed5de5a47a33922742bc3424/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/c6bc34ed5de5a47a33922742bc3424/.command.run
==> STAGING COMPLETE (4 inputs)

Determining HRD-LOH, LST, TAI 
scarHRD input saved for custom_Sig_18_tumor_normal
building scarHRD command
Rscript -e 'library(data.table);library(scarHRD);df <- scar_score("./custom_Sig_18_tumor_normal.scarHRD.input.txt", reference = "grch38", seqz=FALSE);dimnames(df) <- list(NULL, c("LOH","TAI","LST","HRD_score"));fwrite(as.data.table(df), "./custom_Sig_18_tumor_normal.scarHRD.output.score.csv")'
Running scarHRD