[SOLVED] probABEL error

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sdolson494
Posts: 2
Joined: Fri Feb 05, 2016 7:28 pm

[SOLVED] probABEL error

Postby sdolson494 » Fri Feb 05, 2016 7:37 pm

Hello All,

I am new to the forum and have run into an interesting error with probABEL. probABEL is calculating and creating output files without error for every single chromosome and chunk except 1. Chromosome 2, my chunk 58 keeps throwing the error "No digits found while reading genetic data (individual 444, position 61591)". I re-created the dose file and the phenotype file since this usually works in fixing the error but that didn't work. Since this probABEL is on a SGE server I used an interactive session to create the dose and phenotype file to re-run the probABEL analysis, this usually works if the previous troubleshooting doesn't. The error is still persisting. Yes, the dose file does indeed have data within it and I checked specifically at that individual and position and there is actual data not "NA". Do you guys have any insight as to why this error is still persisting? Especially only for this chromosome and chunk.

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: probABEL error

Postby lckarssen » Fri Feb 05, 2016 11:20 pm

Hi,

It looks like you already did quite a few things trying to solve the issue.
Let me check a few assumptions :
  • you try to read from DatABEL files, right?
  • which version of ProbABEL do you use?

Dou you by any chance know what the data is at the indicated location? You could use the DatABEL package to see what is in the .fvi/.fvd file.
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Lennart Karssen
PolyOmica
The Netherlands
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sdolson494
Posts: 2
Joined: Fri Feb 05, 2016 7:28 pm

Re: probABEL error

Postby sdolson494 » Mon Feb 08, 2016 3:47 pm

Hi, I ended up figuring it out over the weekend. I found an error in file conversion during post imputation that was inputting 2,000 instead of 2.000. Once I fixed that and re-created the dose files the issue was resolved.

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: probABEL error

Postby lckarssen » Fri Feb 19, 2016 9:02 pm

Glad to hear you figured it out! Thanks for letting us know.
-------
Lennart Karssen
PolyOmica
The Netherlands
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