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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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sample files for each step? #6

Closed cteenis closed 4 years ago

cteenis commented 8 years ago

HI, I am new to PSMC and followed the commands in the README for a test run. However, I received an error msg same as described in "#4 Rho and theta zero". I want to figure out what went wrong and one thing I can think of is to compare all the intermediate files with a "standard" sample file. Is it possible that you can add some sample files for each step? Thanks.

willright28 commented 5 years ago

hi @cteenis , have you solved this problem? Cuz I'm having the same problem as yours... Thanks in advance!

cteenis commented 5 years ago

hi @cteenis , have you solved this problem? Cuz I'm having the same problem as yours... Thanks in advance!

Dear @willright28 , unfortunately I do not remember how exactly I solved this specific problem as I had run into several problems back then. What I can remember is that you need to use *samtools-0.1.x instead of samtools-1.x (same for bcftools, vcftools.pl). Hope this can be helpful!

willright28 commented 5 years ago

Thanks for the help a lot!

---Original--- From: "cteenis"<notifications@github.com> Date: 2019/9/5 11:23:18 To: "lh3/psmc"<psmc@noreply.github.com>; Cc: "willright28"<854751714@qq.com>;"Mention"<mention@noreply.github.com>; Subject: Re: [lh3/psmc] sample files for each step? (#6)

hi @cteenis , have you solved this problem? Cuz I'm having the same problem as yours... Thanks in advance!

Dear @willright28 , unfortunately I do not remember how exactly I solved this specific problem as I had run into several problems back then. What I can remember is that you need to use *samtools-0.1.x instead of samtools-1.x (same for bcftools, vcftools.pl). Hope this can be helpful!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

GabrieleNocchi commented 4 years ago

Thanks for the help a lot! … ---Original--- From: "cteenis"<notifications@github.com> Date: 2019/9/5 11:23:18 To: "lh3/psmc"<psmc@noreply.github.com>; Cc: "willright28"<854751714@qq.com>;"Mention"<mention@noreply.github.com>; Subject: Re: [lh3/psmc] sample files for each step? (#6) hi @cteenis , have you solved this problem? Cuz I'm having the same problem as yours... Thanks in advance! Dear @willright28 , unfortunately I do not remember how exactly I solved this specific problem as I had run into several problems back then. What I can remember is that you need to use *samtools-0.1.x instead of samtools-1.x (same for bcftools, vcftools.pl). Hope this can be helpful! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

Did you find a solution?

willright28 commented 4 years ago

Thanks for the help a lot! … ---Original--- From: "cteenis"[notifications@github.com](mailto:notifications@github.com) Date: 2019/9/5 11:23:18 To: "lh3/psmc"[psmc@noreply.github.com](mailto:psmc@noreply.github.com); Cc: "willright28"[854751714@qq.com](mailto:854751714@qq.com);"Mention"[mention@noreply.github.com](mailto:mention@noreply.github.com); Subject: Re: [lh3/psmc] sample files for each step? (#6) hi @cteenis , have you solved this problem? Cuz I'm having the same problem as yours... Thanks in advance! Dear @willright28 , unfortunately I do not remember how exactly I solved this specific problem as I had run into several problems back then. What I can remember is that you need to use *samtools-0.1.x instead of samtools-1.x (same for bcftools, vcftools.pl). Hope this can be helpful! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

Did you find a solution?

hi @GabrieleNocchi I tried samtools-0.1.18 and it worked. Hope this can be helpful.