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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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fail on CN_to_VCF step #26

Closed alkodsi closed 8 years ago

alkodsi commented 9 years ago

ascatNgs fails on CN_to_VCF at the end of the run with the following error: "/usr/bin/perl /opt/share/ascatNgs/bin/CN_to_VCF.pl -o xx.copynumber.caveman.vcf -r/human_g1k_v37.fasta -i tumor.copynumber.caveman.csv -sbm tumor.bam -sbw normal.bam" unexpectedly returned exit value 1 at (eval 319) line 13. at /opt/share/ascatNgs/lib/perl5/PCAP/Threaded.pm line 207

running the command gives: ERROR: rs|reference-species must be defined.

If species defined by -rs, it will complain about assembly and if assembly defined, it will complain about platform.

My bam header looks like this @RG ID:1 PL:Illumina PU:machine1 LB:library1 SM:tumor @PG ID:bwa PN:bwa VN:0.5.9-r16

I don't need the VCF output, I just want the run to complete successfully.

keiranmraine commented 9 years ago

Specify species, assembly and platform. It's a minor oversight in the code. FYI 'Illumina' is not technically valid according to the SAM/BAM specification it should be 'ILLUMINA'

alkodsi commented 9 years ago

Thanks. these parameters cannot be passed to ascat.pl. So what should I do?

alkodsi commented 9 years ago

sorry, I just found the parameters. Will try that

alkodsi commented 9 years ago

After trying passing all the parameters, some samples finished successfully, some returned error code 25 without any further details and other failed at the indexing step (tabix) with error unsorted input file.

alkodsi commented 9 years ago

It turned out that my custom probes have positions in chrY and ascat has a hardcoded segment in chromosome Y appended to the segmentation which in some cases disturbs the sorting. I removed chrY probes and it worked.