VCF-VCFintersect error - invalid literal for int() with base 10: 'false'

2.2 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I don't think this is a problem with the input file. I just tried the tool on main and can confirm that it gives the above error, but to me it looks like a bug in parsing the tool parameters. When I enable advanced options for the tool I'm getting a slightly different error: ValueError: invalid literal for int() with base 10: 'use_adv_controls'

so the parsing problem seems to be with the advanced options. Björn Grüning committed a change to the devteams repo addressing parsing of exactly this parameter in July, but the tool on main doesn't seem to be updated yet.

Best, Wolfgang

ADD REPLY • link written 2.2 years ago by Wolfgang Maier • 600

Hi Jen, Thanks for the reply. I don’t think there is anything wrong with the inputs. I’ve used these exact vcf files with this exact tool before on Main and the job ran successfully. The vcf files have not been altered since the last time I ran the job. I’m not using any advanced options. Thanks so much for looking into this. Marcy

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Monday, September 12, 2016 3:11 PM To: Vana, Marcy Subject: [galaxy-biostar] VCF-VCFintersect error - invalid literal for int() with base 10: 'false'

Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org

User Jennifer Hillman Jacksonhttp://biostar.usegalaxy.org/u/254/ wrote Answer: VCF-VCFintersect error - invalid literal for int() with base 10: 'false'http://biostar.usegalaxy.org/p/19440/#19449:

Hello,

This type of error usually indicates that there is a problem with the inputs.

More help including troubleshooting:

Thanks, Jen, Galaxy team

ADD REPLY • link written 2.2 years ago by vanam • 30

Hello Wolfgang, Would you please send in a bug report from one of the error datasets? Please make sure the job and inputs are undeleted and I'll check all to find out what is going on. https://wiki.galaxyproject.org/Support#Reporting_tool_errors Please include a link to this Biostars post in the comments.

Thanks, Jen, Galaxy team

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I filed the report. Thanks, Wolfgang

ADD REPLY • link written 2.2 years ago by Wolfgang Maier • 600

Hello Marcy, Would you please do the same - send in a bug report from the error dataset. https://wiki.galaxyproject.org/Support#Reporting_tool_errors Please include a link to this Biostars post in the comments. Thanks, Jen, Galaxy team

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I sent in the bug report. Thanks, Marcy

ADD REPLY • link written 2.2 years ago by vanam • 30

Marcy, Wolfgang - Thanks for sending these in!

I'll be looking at both of your reports and will reply directly to your bug emails with details then put a more generalized answer here back in Biostars. Please be patient - if there was a bug fix, that will complicate things a bit. More feedback soon, Jen

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update:

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

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

The issue was fixed some time ago, just posting status back here as a reference.

Old version: VCF-VCFintersect: Intersect two VCF datasets (Galaxy Version 0.0.3)

Updated version: VCF-VCFintersect: Intersect two VCF datasets (Galaxy Version 1.0.0_rc1+galaxy0)

Make sure to use updated tool version or errors may come up.

This does not come up when launching the tool from the tool panel (a bug we'll be fixing: https://github.com/galaxyproject/galaxy/issues/3021). Switch to the most current wrapper using the "Versions" pull-down menu on the tool form.

ADD REPLY • link modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson ♦ 25k

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