Calculating bootstrap for psmc

Question

[gubrins]

Heys,

I'm trying to perform some bootstrap for the program PSMC (https://github.com/lh3/psmc) but I get this message:

Segmentation fault (core dumped)

When running this code:

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

I was checking what xargs is doing and the -i option is for replacing, so I'm not really sure if I'm doing something wrong or it is outdated.

Any help will be gladly welcomed!

Answer 1

[ziwei.liu]

The README file made a small mistake. It should be 'split.psmcfa' but not 'split.fa' in the command line. Like this

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

But not this

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