Hi, I'm trying to run a VCF-VCFintersect job I've run before and the job is failing with this error: invalid literal for int() with base 10: 'false'. I'm using vcf files that I've used before with this job. Is it possible there is something wrong with the tool? I'm using Main. Thanks, Marcy
This type of error usually indicates that there is a problem with the inputs.
Check the chromosome names in the VCF files against each other and any other data used. For example, the chromosome identifiers in the reference genome, whether native or custom, must contain only the chromosome name in the title line (">") with no description content. Any native genome indexed on http://usegalaxy.org are in this format. Custom genome fasta files often are not when issues come up.
More help including troubleshooting:
Thanks, Jen, Galaxy team
Wolfgang is correct in that the tool had a bug fix that did not get promoted to the Tool Shed repo or to Galaxy Main/Test.
Our team is working to get the tool updated right now. Please follow this ticket for progress: https://github.com/galaxyproject/tools-devteam/issues/391
Thanks to you both for reporting the problem! Jen, Galaxy team