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Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
GNU General Public License v3.0
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ZeroDivisionError: float division by zero, new "old" error #87

Open cbossu opened 6 months ago

cbossu commented 6 months ago

Hello, I know there was an older post related to this (it's currently closed), but this has only recently become an issue for us. My collaborators are getting the following error when running the newer version of pcangd (v1.21). We have converted an imputed vcf file (no missing data) to a bed file in plink, and we are running pcangsd --admix across multiple values of -e. The error, attached below, shows pcangsd is reading the plink file.

Parsing PLINK files. Loaded 1872314 sites and 121 individuals. Estimating minor allele frequencies. Traceback (most recent call last): File "/usr/local/Dist/anaconda-WGSassign/envs/WGSassign/bin/pcangsd", line 8, in sys.exit(main()) File "/usr/local/Dist/anaconda-WGSassign/envs/WGSassign/lib/python3.10/site-packages/pcangsd/pcangsd.py", line 219, in main f = shared.emMAF(L, args.maf_iter, args.maf_tole, args.threads) File "/usr/local/Dist/anaconda-WGSassign/envs/WGSassign/lib/python3.10/site-packages/pcangsd/shared.py", line 50, in emMAF alpha = -max(1.0, sqrt(sr2/sv2)) ZeroDivisionError: float division by zero

Note that I do not get this error when I run --admix on an earlier pcangsd version (1.11). We are using the same data set. Any ideas on why this would be happening with the newer version of pcangsd?

Thanks,

Christen

Rosemeis commented 6 months ago

Hi,

Sorry for the late reply. The issue arises after I added some speed-up, which assumes there are some missingness present. But I have just pushed an update here on GitHub. Let me know if it helped! :-)

Best, Jonas