--sites_save options reports only 0s

Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.

GNU General Public License v3.0

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Closed shyama-mama closed 3 months ago

shyama-mama commented 3 months ago

Hi guys,

I am using the v1.2 release of pcangsd. The log file indicates 7388691 sites loaded out of 8815455

Number of sites after MAF filtering (0.05): 7388691

The command was run as follows:

pcangsd -b ${BEAGLE} -e 2 -t 64 -o ${OUTPUT} --selection --admix --sites_save --filter ${FILE}

However, the sites_save output looks like this

sort ${SITES_SAVE} | uniq -c 
8815455 0

Do you know what could be happening here?

Thanks, Shyam

shyama-mama commented 3 months ago

Nvm it was fixed using the latest version v1.21 built from the master branch. Thanks I'll close this ticket now.