Comments (5)
laninsky
commented on July 27, 2024
Hi Carla - is the example dataset working for you? After confirming that it is (i.e. your installation is all good), I think I'll need to your input files to try and pinpoint where the error is creeping in.
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carlahurt
commented on July 27, 2024
Thank you for your quick response! I ran the example file successfully, so it must be something with my input files. I'm attaching my logfile, VCF, GBS_SNP_Filter.txt, and popmap.txt file here.
I appreciate any suggestions you might have.
popmap.txt
GBS_SNP_filter.txt
BTM.vcf.txt
slurm-1542889.out.txt
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laninsky
commented on July 27, 2024
Hi Carla - heaps of apologies on the length of time on this, but I've been away from the office - back on it and trying to sleuth out what is going on. Please feel free to pester if you haven't heard back from me in a week!
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carlahurt
commented on July 27, 2024
Hi Alana,
Thank you for getting back to me. While I couldn't figure out what happened with that dataset, I reran ipyrad and my new VCF files runs perfectly on GBS_SNP filter. This program is a lifesaver. Thank you so much for making it available.!
Carla Hurt
Associate Professor of Biology
Tennessee Tech University
(931) 372-3143
https://sites.tntech.edu/hurtlab
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Cc: Hurt, Carla ***@***.***>; Author ***@***.***>
Subject: Re: [laninsky/GBS_SNP_filter] Error using HWE.R (Issue #14)
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Hi Carla - heaps of apologies on the length of time on this, but I've been away from the office - back on it and trying to sleuth out what is going on. Please feel free to pester if you haven't heard back from me in a week!
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laninsky
commented on July 27, 2024
Ha! OK, given that magically solved the issue I'll close this issue for now, but if it crops up again let me know, and I'll resume the sleuthing.
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Related Issues (11)
- Error in -removepops HOT 14
- unknown issue HOT 6
- Error in generating .HWE.vcf file HOT 4
- Failing after PLINK for stickleback test data HOT 1
- Add some guidance on what vcf to use
- Error in generating the .ld.vcf file (the final step) HOT 4
- Check the formatting of the vcf
- Address some deprecating in code HOT 1
- ld performance in the package HOT 2
- locus ID regex pattern when column has colons HOT 5
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