VCFFilter 1.0.0 fatal error with FreeBayes VCF input

Question: VCFFilter 1.0.0 fatal error with FreeBayes VCF input

6 months ago by

When running a vcf file (output was from FreeBayes tool), I am getting the fatal error

Fatal error: Exit code 134 () terminate called after throwing an instance of 'std::out_of_range'   
what():  basic_string::substr: __pos (which is 1) > this->size() (which is 0) /galaxy-repl/main/jobdir/019/620/19620417/tool_script.sh: line 41: 33442 
Aborted                 (core dumped) vcffilter input1.vcf.gz > '/galaxy-repl/main/files/025/459/dataset_25459284.dat'

How do I proceed, please help

vcffilter vcf 1.0.0 galaxy freebayes • 269 views

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modified 6 months ago • written 6 months ago by premraj.preeti • 10

Related post: VCFFilter tool update from version 1.0.0 to 0.0.3 https://biostar.usegalaxy.org/p/28211/

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This usage error can come up when an unsorted BAM is an input to the tool, the filter criteria are set in a way that filters out all of the alignments, or a field is filtered on that does not exist in the VCF. There can be other reasons, but those are the most common.

Please review the troubleshooting help and example tutorials below to better understand usage and solutions.

Support FAQs: https://galaxyproject.org/support/#unexpected-results
Galaxy tutorials, including those for variant analysis that include Freebayes: https://galaxyproject.org/learn/

If you cannot solve the problem, please send in a bug report following the instructions in the FAQs.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Sorry, I see your bug report from yesterday. I'll send feedback via email.

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Replied with the correct term filter to use. Please test it out - it worked for me using your same tutorial data but if not for you, we can follow up and get it right.

Side issue: the tool form help needs an update to reflect the new way that options are modeled. I created a ticket for that and requested better error messages. This specific issue (malformed terms) is confusing for many. If interested, please see: https://github.com/galaxyproject/tools-iuc/issues/1910

Tutorials that include older tools can be difficult to update when hosted at certain external sources or when included in videos. Things change fast. So, it is good to play around with the options when a tool looks different as a first pass solution. And you can always ask for help when you cannot figure it out.

Thanks for reporting this & sending in the bug report, it was the only way to find out what was really going wrong.

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

6 months ago by

premraj.preeti • 10

premraj.preeti • 10 wrote:

Thanks a ton Jennifer. This is very helpful

ADD COMMENT • link written 6 months ago by premraj.preeti • 10

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