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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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Confusing typo in the REAME file #13

Open willyrv opened 4 years ago

willyrv commented 4 years ago

Hello Li,

There is a small typo in the REAME file that may be confusing. In the bootstrapping example, you produce a file named "split.psmcfa" with the command

             utils/splitfa diploid.psmcfa > split.psmcfa

But the next command

     seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" \
    -o round-{}.psmc split.fa | sh

takes as input the file "split.fa" which does not exist. Should it be "split.psmcfa" ?

Thanks,

Willy

DeondeJager commented 4 years ago

Hi @willyrv,

You've probably already solved this, but yes, it should be "split.psmcfa".

Also, just in case you or anyone else is having an issue with running PSMC in parallel for bootstrapping, as I was until recently on our computing cluster, add -P number_of_cores to the command and remove the word "echo". So the command would look like this:

seq 100 | xargs -P 24 -i psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" -o round-{}.psmc split.psmcfa | sh where -P 24 means using 24 cores or threads.

Cheers Deon