Atarva error on trexplorer catalog

[elbayaliyev]

Dear Sowpati Lab,

We run into error while trying to run trexplorer catalog using atarva.
https://trexplorer.broadinstitute.org/

Basically what happened is catalog we are trying to genotype is 5.5m. Output VCF contains only 7k regions that are genotyped. Atarva runs and generate VCF without any errors.

One thing i saw that break happen here:

Because next regions are not genotyped in vcf file:

Attaching log files, output log file,vcf file and command:

.command.log
.command.sh
HG001.PAW79146.haplotagged.URfix.atarva_debug.log
HG001.PAW79146.haplotagged.URfix.atarva.vcf.log

[sowpati]

Dear @elbayaliyev

Thanks for raising this issue. From the log, it appears that the motif decomposition is failing for some reason. Before we debug this further, could you please check at your earliest convenience if the issue persists when repeated with the --decompose flag set to false?

Thank you in advance.

[elbayaliyev]

Dear @sowpati ,

Thank you for quick response.

I run without decompose flag and i can confirm that it works.

It is still running but from simple look at work folder i can see that more regions genotyped currently compared to run using decompose flag.

Thanks,
Elbay

[elbayaliyev]

Update. Atarva run done succesfully.

[Dhaksnamoorthy]

Hi @elbayaliyev,
Thanks for confirming the issue. The fix is now available in v0.4.0, currently pushed to the dev branch. If you happen to test the dev version, please let us know if it works as expected. We will soon be merging it with the master branch.