Error in implement_ascat: dim(X) must have a positive length

[imendes93]

Greetings,

I'm attempting to run ascatNgs and I'm running into the following error:

HREAD_EXITED: General output can be found in this file, last 10 lines below: /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.out
STDOUT: [1] Reading Tumor LogR data...
STDOUT: [1] Reading Tumor BAF data...
STDOUT: [1] Reading Germline LogR data...
STDOUT: [1] Reading Germline BAF data...
STDOUT: [1] Registering SNP locations...
STDOUT: [1] Splitting genome in distinct chunks...
STDOUT: [1] Sample pb_sample (1/1)

THREAD_EXITED: Errors can be found in this file, output below: /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.err

STDERR: + cut -f 1-3 /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/SnpGcCorrections.tsv
STDERR: + cd /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/ascat
STDERR: + /usr/bin/Rscript /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat/runASCAT.R /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/SnpPositions.tsv /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/SnpGcCorrections.tsv pb_sample pb_sample.count pb_sample pb_sample.count XY 24 /tmp/nxf-3672569323515647077/outdir/ascat/tmpAscat/ascat/pb_sample.Rdata 'c('\''chr1'\'','\''chr10'\'','\''chr11'\'','\''chr12'\'','\''chr13'\'','\''chr14'\'','\''chr15'\'','\''chr16'\'','\''chr17'\'','\''chr18'\'','\''chr19'\'','\''chr2'\'','\''chr20'\'','\''chr21'\'','\''chr22'\'','\''chr3'\'','\''chr4'\'','\''chr5'\'','\''chr6'\'','\''chr7'\'','\''chr8'\'','\''chr9'\'','\''chrX'\'','\''chrY'\'')' 'c('\''1'\'','\''10'\'','\''11'\'','\''12'\'','\''13'\'','\''14'\'','\''15'\'','\''16'\'','\''17'\'','\''18'\'','\''19'\'','\''2'\'','\''20'\'','\''21'\'','\''22'\'','\''3'\'','\''4'\'','\''5'\'','\''6'\'','\''7'\'','\''8'\'','\''9'\'','\''X'\'','\''Y'\'')'
STDERR: Error in apply(corr_tot, 1, function(x) sum(abs(x * length_tot))/sum(length_tot)) : 
STDERR:   dim(X) must have a positive length
STDERR: Calls: ascat.GCcorrect -> apply
STDERR: Execution halted
STDERR: Command exited with non-zero status 1
STDERR: 157.74user 2.04system 2:39.79elapsed 99%CPU (0avgtext+0avgdata 2620972maxresident)k
STDERR: 0inputs+437232outputs (0major+773683minor)pagefaults 0swaps

Here's the command that i'm using:

ascat.pl \
    -outdir outdir/ascat \
    -tumour pb_tumor.bam \
    -normal pb_normal.bam \
    -snp_gc SnpGcCorrections.tsv\
    -reference Homo_sapiens_assembly38.fasta \
    -minbasequal 20 \
    -gender XY  \
    -gc chrY \
    -species human \
    -assembly GRCh38 \
    -pr WGS \
    -pl ILLUMINA \
    -c 4 \
    -force

In the container quay.io/wtsicgp/ascatngs:4.5.0. The index for the bam files and reference are in the directory.

The input files are publicly available at s3://eu-west-1-example-data/nihr/testdata
Thank you for your assistance!

[keiranmraine]

Highly likely this is the same issue as: cancerit/cgpPindel#100