CCRGeneticsBranch / Oncogenomics_NF_WF

https://ccrgeneticsbranch.github.io/Oncogenomics_NF_WF/
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Error in data frame - cosmicsignature #27

Open vinegang opened 9 months ago

vinegang commented 9 months ago

Some of the exome samples have the following error.

ERROR ~ Error executing process > 'Tumor_Normal_WF:Cosmic3Signature (COAD_Patient5)'

Caused by:
  Process `Tumor_Normal_WF:Cosmic3Signature (COAD_Patient5)` terminated with an error exit status (1)

Command executed:

  TMP=tmp/
  mkdir $TMP
  trap 'rm -rf "$TMP"' EXIT

  mv COAD_Patient5_T5C_E.MuTect.raw.vcf COAD_Patient5_T5C_E.strelka.indels.raw.vcf COAD_Patient5_T5C_E.strelka.snvs.raw.vcf $TMP
  matrixgenerator.py COAD_Patient5_T5C_E $TMP
  cut -f1 $TMP/output/ID/COAD_Patient5_T5C_E.ID83.all |awk -F ":" -v OFS="_" '{print $2,$3,$1,$4}'|sed  s'/Del/DEL/g'|sed s'/Ins/INS/g' |sed s'/__MutationType_/MutationType/g'|sed s'/_R_/_repeats_/g'|sed s'/_M_/_MH_/g'| sed s'/5/5+/g' |paste - $TMP/output/ID/COAD_Patient5_T5C_E.ID83.all|cut -f1,3 > $TMP/output/ID/COAD_Patient5_T5C_E.ID83.all_updatedcolumns
  deconstructsigs_indels.R $TMP/output/ID/COAD_Patient5_T5C_E.ID83.all_updatedcolumns COAD_Patient5_T5C_E.Indel83 signatures.indels.cosmic.v3.may2019.rda
  deconstructsigs_sbs.R $TMP/output/SBS/COAD_Patient5_T5C_E.SBS96.all COAD_Patient5_T5C_E.SBS96 signatures.genome.cosmic.v3.may2019.rda
  deconstructsigs_dbs.R $TMP/output/DBS/COAD_Patient5_T5C_E.DBS78.all COAD_Patient5_T5C_E.DBS78 signatures.dbs.cosmic.v3.may2019.rda

Command exit status:
  1

Command output:
  Starting matrix generation for SNVs and DINUCs...There may be an issue with the formatting of your matrix file.
  There may be an issue with the formatting of your matrix file.
  There may be an issue with the formatting of your matrix file.
  Completed! Elapsed time: 9.47 seconds.
  Starting matrix generation for INDELs...There may be an issue with the formatting of your matrix file.
  Completed! Elapsed time: 1.74 seconds.
  Matrices generated for 1 samples with 0 errors. Total of 103686 SNVs, 1588 DINUCs, and 100 INDELs were successfully analyzed.
  null device 
            1 
  [1] "list"
  null device 
            1 
  null device 
            1 
  [1] "list"
  null device 
            1 
  null device 
            1 
  [1] "list"

Command error:
  The following objects are masked from 'package:base':

      aperm, apply, rowsum

  Loading required package: Rsamtools

  Attaching package: 'VariantAnnotation'

  The following object is masked from 'package:base':

      tabulate

  Attaching package: 'BSgenome.Hsapiens.UCSC.hg38'

  The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg19':

      Hsapiens

  -- Attaching core tidyverse packages ------------------------ tidyverse 2.0.0 --
  v dplyr     1.1.2     v readr     2.1.4
  v forcats   1.0.0     v stringr   1.5.0
  v ggplot2   3.4.2     v tibble    3.2.1
  v lubridate 1.9.2     v tidyr     1.3.0
  v purrr     1.0.2     
  -- Conflicts ------------------------------------------ tidyverse_conflicts() --
  x lubridate::%within%() masks IRanges::%within%()
  x ggplot2::Position()   masks BiocGenerics::Position(), base::Position()
  x dplyr::collapse()     masks Biostrings::collapse(), IRanges::collapse()
  x dplyr::combine()      masks Biobase::combine(), BiocGenerics::combine()
  x purrr::compact()      masks XVector::compact()
  x dplyr::count()        masks matrixStats::count()
  x dplyr::desc()         masks IRanges::desc()
  x tidyr::expand()       masks VariantAnnotation::expand(), S4Vectors::expand()
  x dplyr::filter()       masks stats::filter()
  x dplyr::first()        masks S4Vectors::first()
  x stringr::fixed()      masks VariantAnnotation::fixed()
  x dplyr::lag()          masks stats::lag()
  x purrr::reduce()       masks GenomicRanges::reduce(), IRanges::reduce()
  x dplyr::rename()       masks S4Vectors::rename()
  x lubridate::second()   masks S4Vectors::second()
  x lubridate::second<-() masks S4Vectors::second<-()
  x dplyr::select()       masks VariantAnnotation::select()
  x purrr::simplify()     masks DelayedArray::simplify()
  x dplyr::slice()        masks XVector::slice(), IRanges::slice()
  i Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
  Error in data.frame(missing.colors, add.color) : 
    arguments imply differing number of rows: 0, 1
  Calls: makePie -> data.frame
  Execution halted

Work dir:
  /vf/users/khanlab/projects/processed_DATA/COAD_Patient5/COAD_Patient5_T5C/work/db/f3746e3524b705e38d3ee628f0a8fd
vinegang commented 9 months ago

debug folder: /vf/users/khanlab/projects/processed_DATA/COAD_Patient4/COAD_Patient4_T4C/work/d3/20ab8bc7487cf19b2a8f779152b6fe