.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e5389f1f7ffb69cc3ebeeed16d3f25/.command.log
Size: 962 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/454b7e0491fa3cc91887bb29aef54f/HCC1395_tumor_vs_HCC1395_BL.segments.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/454b7e0491fa3cc91887bb29aef54f/HCC1395_tumor_vs_HCC1395_BL.purity_ploidy.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e5389f1f7ffb69cc3ebeeed16d3f25/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e5389f1f7ffb69cc3ebeeed16d3f25/.command.run
==> STAGING COMPLETE (4 inputs)

Determining HRD-LOH, LST, TAI 
scarHRD input saved for HCC1395_tumor_vs_HCC1395_BL
building scarHRD command
Rscript -e 'library(data.table);library(scarHRD);df <- scar_score("./HCC1395_tumor_vs_HCC1395_BL.scarHRD.input.txt", reference = "grch38", seqz=FALSE);dimnames(df) <- list(NULL, c("LOH","TAI","LST","HRD_score"));fwrite(as.data.table(df), "./HCC1395_tumor_vs_HCC1395_BL.scarHRD.output.score.csv")'
Running scarHRD