cannot read glf

[z0on]

Hi Felipe - I am sure it is something silly, but I am out of ideas... For some reason I cannot get this to work:

NIND=cat bams.nr | wc -l
NS=zcat g3.mafs.gz | wc -l
zcat g3.glf.gz | ngsF --glf - --n_ind $NIND --n_sites $NS --out inbr

I'm getting "ERROR: cannot read GLF file!"

I made sure to make g3.glf.gz with -doGlf 3. What am I doing wrong?
I have the most recent angsd, version 0.933-25-g5955d69 (htslib: 1.9-44-g80f3557)

cheers
Misha

[fgvieira]

I don't think the error is because of this, but it is worth a try.
I think the NS should be:

NS=$((`zcat g3.mafs.gz | wc -l`-1))

since the MAFs file has a header.

[z0on]

Damn, you are right! problem solved, thanks! Misha

…

On Mon, Jun 8, 2020 at 4:45 AM Filipe G. Vieira ***@***.***> wrote: I don't think the error is because of this, but it is worth a try. I think the NS should be: NS=$((`zcat g3.mafs.gz | wc -l`-1)) since the MAFs file has a header. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGEBNMQIXPNABSZFYSLRVSXLJANCNFSM4NNKL4IQ> .