Question: VCF-VCFintersect error - invalid literal for int() with base 10: 'false'
2
gravatar for vanam
19 months ago by
vanam30
United States
vanam30 wrote:

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

ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson24k • written 19 months ago by vanam30
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 19 months ago by Jennifer Hillman Jackson24k
1

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 REPLYlink written 19 months ago by Wolfgang Maier530
1

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.

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 REPLYlink written 19 months ago by vanam30

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 REPLYlink modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson24k

Hi Jen, I filed the report. Thanks, Wolfgang

ADD REPLYlink written 19 months ago by Wolfgang Maier530

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 REPLYlink written 19 months ago by Jennifer Hillman Jackson24k

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

ADD REPLYlink written 19 months ago by vanam30

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 REPLYlink written 19 months ago by Jennifer Hillman Jackson24k
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 19 months ago by Jennifer Hillman Jackson24k
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