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gphocs-dev / G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.
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Error while processing alignments #73

Open willright28 opened 3 years ago

willright28 commented 3 years ago

Hi, I got a error meesage while running the gphocs, please see blow:

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G-Phocs version 1.3.2,  Oct. 2017

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Setting Thread Count to: 5
Reading control settings from file cczm.ctl...
Done.
Reading sequence data...  1000 loci, as specified in sequence file CCZM.gphocs.out.
Reading loci (.=100 loci): .......... Error: Number of phased patterns is negative, unable to process het patterns for genealogy 213.
Error while processing alignments:
Error while reallocating space for phasedPatternArray.

Could anyone help me with that? Thanks in advanced!

igronau commented 3 years ago

This error message indicates that the number of distinct phased patterns you have in one of your loci exceeds the maximum that G-PhoCS assumes. This typically happens when you try to analyze many individuals and have high heterozygosity rates. Note that every site is expanded to ~ 2^(k-1) sites, where k is the number of heterozygous genotypes observed in that site. If you're trying to analyze more than 30 individuals, then prune down your sample set. Another potential cause for this error is if your loci are too long. Locus length should not exceed 1 kb.