_-[nf-core/sarek] Pipeline completed with errors-
[27/e13d07] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT (CGMH-FH-RCC1T_vs_CGMH-FH-RCC1N)` terminated with an error exit status (1) -- Execution is retried (7)
Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT (CGMH-FH-RCC1T_vs_CGMH-FH-RCC1N)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT (CGMH-FH-RCC1T_vs_CGMH-FH-RCC1N)` terminated with an error exit status (1)

Command executed:

  #!/usr/bin/env Rscript
  library(RColorBrewer)
  library(ASCAT)
  options(bitmapType='cairo')
  
  #build prefixes: <abspath_to_files/prefix_chr>
  allele_path = normalizePath("G1000_alleles_hg19")
  allele_prefix = paste0(allele_path, "/", "G1000_alleles_hg19", "_chr")
  
  loci_path = normalizePath("G1000_loci_hg19")
  loci_prefix = paste0(loci_path, "/", "G1000_loci_hg19", "_chr")
  
  #prepare from BAM files
  ascat.prepareHTS(
      tumourseqfile = "T.converted.cram",
      normalseqfile = "N.converted.cram",
      tumourname = paste0("T_vs_N", ".tumour"),
      normalname = paste0("T_vs_N", ".normal"),
      allelecounter_exe = "alleleCounter",
      alleles.prefix = allele_prefix,
      loci.prefix = loci_prefix,
      gender = "XY",
      genomeVersion = "hg19",
      nthreads = 16
      ,minCounts = 10
      ,BED_file = 'wgs_calling_regions_Sarek.list'
      ,chrom_names = c(1:22, 'X', 'Y')
      ,min_base_qual = 20
      ,min_map_qual = 35
      ,ref.fasta = 'human_g1k_v37_decoy.fasta'
  
  
  )
  
  
  #Load the data
  ascat.bc = ascat.loadData(
      Tumor_LogR_file = paste0("T_vs_N", ".tumour_tumourLogR.txt"),
      Tumor_BAF_file = paste0("T_vs_N", ".tumour_tumourBAF.txt"),
      Germline_LogR_file = paste0("T_vs_N", ".tumour_normalLogR.txt"),
      Germline_BAF_file = paste0("T_vs_N", ".tumour_normalBAF.txt"),
      genomeVersion = "hg19",
      gender = "XY"
  )
  
  #Plot the raw data
  ascat.plotRawData(ascat.bc, img.prefix = paste0("T_vs_N", ".before_correction."))
  
  # optional LogRCorrection
  if("GC_G1000_hg19" != "NULL") {
      gc_input = paste0(normalizePath("GC_G1000_hg19"), "/", "GC_G1000_hg19", ".txt")
  
      if("RT_G1000_hg19" != "NULL"){
          rt_input = paste0(normalizePath("RT_G1000_hg19"), "/", "RT_G1000_hg19", ".txt")
          ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = rt_input)
          #Plot raw data after correction
          ascat.plotRawData(ascat.bc, img.prefix = paste0("T_vs_N", ".after_correction_gc_rt."))
      }
      else {
          ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = RT_G1000_hg19)
          #Plot raw data after correction
          ascat.plotRawData(ascat.bc, img.prefix = paste0("T_vs_N", ".after_correction_gc."))
      }
  }
  
  #Segment the data
  ascat.bc = ascat.aspcf(ascat.bc)
  
  #Plot the segmented data
  ascat.plotSegmentedData(ascat.bc)
  
  #Run ASCAT to fit every tumor to a model, inferring ploidy, normal cell contamination, and discrete copy numbers
  #If psi and rho are manually set:
  if (!is.null(NULL) && !is.null(NULL)){
      ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=NULL, psi_manual=NULL)
  } else if(!is.null(NULL) && is.null(NULL)){
      ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=NULL)
  } else if(!is.null(NULL) && is.null(NULL)){
      ascat.output <- ascat.runAscat(ascat.bc, gamma=1, psi_manual=NULL)
  } else {
      ascat.output <- ascat.runAscat(ascat.bc, gamma=1)
  }
  
  #Extract metrics from ASCAT profiles
  QC = ascat.metrics(ascat.bc,ascat.output)
  
  #Write out segmented regions (including regions with one copy of each allele)
  write.table(ascat.output[["segments"]], file=paste0("T_vs_N", ".segments.txt"), sep=" ", quote=F, row.names=F)
  
  #Write out CNVs in bed format
  cnvs=ascat.output[["segments"]][2:6]
  write.table(cnvs, file=paste0("T_vs_N",".cnvs.txt"), sep="    ", quote=F, row.names=F, col.names=T)
  
  #Write out purity and ploidy info
  summary <- tryCatch({
          matrix(c(ascat.output[["aberrantcellfraction"]], ascat.output[["ploidy"]]), ncol=2, byrow=TRUE)}, error = function(err) {
              # error handler picks up where error was generated
              print(paste("Could not find optimal solution:  ",err))
              return(matrix(c(0,0),nrow=1,ncol=2,byrow = TRUE))
      }
  )
  colnames(summary) <- c("AberrantCellFraction","Ploidy")
  write.table(summary, file=paste0("T_vs_N",".purityploidy.txt"), sep=" ", quote=F, row.names=F, col.names=T)
  
  write.table(QC, file=paste0("T_vs_N", ".metrics.txt"), sep="  ", quote=F, row.names=F)
  
  # version export
  f <- file("versions.yml","w")
  alleleCounter_version = system(paste("alleleCounter --version"), intern = T)
  ascat_version = sessionInfo()$otherPkgs$ASCAT$Version
  writeLines(paste0('"', "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT", '"', ":"), f)
  writeLines(paste("    alleleCounter:", alleleCounter_version), f)
  writeLines(paste("    ascat:", ascat_version), f)
  close(f)

Command exit status:
  1

Command output:
  (empty)

Command error:
  Done reading locis
  Multi pos start:
  Reading locis
  [E::sam_itr_next] Null iterator
  [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region
  [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
  munmap_chunk(): invalid pointer
  Done reading locis
  Multi pos start:
  [E::sam_itr_next] Null iterator
  [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region
  [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
  Reading locis
  Done reading locis
  Multi pos start:
  munmap_chunk(): invalid pointer
  [E::sam_itr_next] Null iterator
  [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error   <<..............>>

Work dir:
  <<..............>>

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`_