Error in calling ascat.GCcorrect

[Soniazumalave]

Hi there, I am trying to run ascat on my data

srun ascat.pl -outdir $OUTDIR -tumour $TUMOR -normal $NORMAL -reference $GENOME \
-snp_gc SnpGcCorrections.tsv -protocol WGS \
-gender XX -genderChr Y -cpus 18

and got an error no matter what SnpGcCorrections reference file I use.

Executing: /opt/cesga/ascatngs/4.0.0/gcc/5.3.0/bin/ascat.pl -outdir ASCAT/M7vsM6 -tumour MCRL007_S7/MCRL007_S7.sorted.dedup.bam -normal MCRL006_S6/MCRL006_S6.sorted.dedup.bam -reference hg19/genome.fa -snp_gc ASCAT/SnpGcCorrections.tsv -protocol WGS -gender XX -genderChr Y -cpus 18
"/usr/bin/time /mnt/lustre/scratch/home/usc/mg/szd/ASCAT/M7vsM6/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.sh 1> /mnt/lustre/scratch/home/usc/mg/szd/ASCAT/M7vsM6/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.out 2> /mnt/lustre/scratch/home/usc/mg/szd/ASCAT/M7vsM6/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.err" unexpectedly returned exit value 1 at /opt/cesga/pcap-core/3.4.1/gcc/5.3.0/lib/perl5/PCAP/Threaded.pm line 229.
 at /opt/cesga/pcap-core/3.4.1/gcc/5.3.0/lib/perl5/PCAP/Threaded.pm line 227
srun: error: c7145: task 0: Exited with exit code 1
srun: Terminating job step 1244346.0

cat /M7vsM6/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.err

/opt/cesga/R/3.4.0/gcc/5.3.0/bin/Rscript /opt/cesga/ascatngs/4.0.0/gcc/5.3.0/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat/runASCAT.R /opt/cesga/ascatngs/4.0.0/gcc/5.3.0/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat /mnt/lustre/scratch/home/usc/mg/szd/ASCAT/M7vsM6/tmpAscat/SnpPositions.tsv /mnt/lustre/scratch/home/usc/mg/szd/ASCAT/M7vsM6/tmpAscat/SnpGcCorrections.tsv Patient_3 Patient_3.count Patient_3 Patient_3.count XX 24 /mnt/lustre/scratch/home/usc/mg/szd/ASCAT/M7vsM6/tmpAscat/ascat/Patient_3.Rdata
Error in apply(corr_tot, 1, function(x) sum(abs(x * length_tot))/sum(length_tot)) : 
  dim(X) must have a positive length
Calls: ascat.GCcorrect -> apply
Execution halted
453.29user 2.62system 7:36.40elapsed 99%CPU (0avgtext+0avgdata 2141944maxresident)k
34928inputs+438728outputs (35major+708846minor)pagefaults 0swaps

What's wrong? I am not able to spot the error. Thank you in advance.

Kind regards, Sonia

[keiranmraine]

A few things to confirm:

• Have you confirmed that the Chromosomes names in your bam files is the same as those in the SnpGcCorrections files? e.g. chr1 vs 1?
• You are using whole genome NGS data and not exome/pullown data?

Beyond this you may need to contact the maintainers of the underlying R library, see this projects README for links to that repository,

[Soniazumalave]

Hi Keiran,

Thank you for getting back. So, regarding your first question, yes, they match (No 'chr'). Although I read extra contigs in the genome.fa file wouldn't be taken into account, I also tried to delete them, but still got the same error. Tried sorting too, but no improvement. And yes, I am using WGS.

Thank you anyway, I will try to contact the maintainers.

Regards, Sonia Z