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fgvieira / ngsF

Estimation of per-individual inbreeding coefficients under a probabilistic framework
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cannot read glf #13

Closed z0on closed 4 years ago

z0on commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

On Mon, Jun 8, 2020 at 4:45 AM Filipe G. Vieira notifications@github.com 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.

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