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z0on / AFS-analysis-with-moments

Standalone python scripts to do pairwise AFS analysis for population differentiation using Moments (http://www.genetics.org/content/early/2017/05/08/genetics.117.200493)
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Issues with running ANGSD with -maxHetFreq filter #5

Closed lexiebsturm closed 4 years ago

lexiebsturm commented 4 years ago

Hi Misha, I am having trouble generating the two pops mafs file needed to generate the SAF data for both populations. When I try to run it, I keep getting error "-maxHetFreq is unknown will exit." At first I thought this was a version issue so I requested that the HPC staff here at FAU update the angsd module. I am now running angsd version: 0.929-19-gb2b41b5 (htslib: 1.9-139-gce7daf7) but still having the same issue. Is there another issue that may be causing the problem? Your advice would be greatly appreciated!

Thanks

z0on commented 4 years ago

Hi Lexie - sorry I missed you last two emails... - congrats on the Mcav paper!!! great job!

maxHetFreq is indeed a new filter - my angsd is 0.933-25-g5955d69 , let them get the newest one!

On Fri, Sep 11, 2020 at 8:09 AM Alexis Sturm notifications@github.com wrote:

Hi Misha, I am having trouble generating the two pops mafs file needed to generate the SAF data for both populations. When I try to run it, I keep getting error "-maxHetFreq is unknown will exit." At first I thought this was a version issue so I requested that the HPC staff here at FAU update the angsd module. I am now running angsd version: 0.929-19-gb2b41b5 (htslib: 1.9-139-gce7daf7) but still having the same issue. Is there another issue that may be causing the problem? Your advice would be greatly appreciated!

Thanks

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lexiebsturm commented 4 years ago

Thanks Misha!! Your 2bRAD workshop/code made it happen :) they updated ANGSD on the cluster and the filter works now. Many thanks, Lexie