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.
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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
Some of the exome samples have the following error.