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HYPHY Package >> HyPhy bugs >> SEGFAULT in TestBranchDNDS.bf with longseq file http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1115904440 Message started by avilella on May 12th, 2005 at 6:27am |
Title: Re: SEGFAULT in TestBranchDNDS.bf with longseq fil Post by Sergei on May 12th, 2005 at 8:37am
Dear Albert,
The analysis was crashing because it was trying to allocate more memory than is addressable by 32 bit machines for cache. Your example file has 147000 unique codon patterns, and a caching scheme in HyPhy wanted to allocate 147000*61*64 (because of 64 rate classes) * 8 (=4591103936) bytes. By asking for 8 rate classes (each for syn and non-syn) you were also attempting to fit 64 rate classes to 4 sequences - I would recommend 3x3 at most (which would also reduce memory allocation by a factor of 64/9). If this fails, try including CACHE_SUBTREES=0; at the beginning of TestBranchDNDS.bf. This flag will turn off the caching scheme (and reduce performance a bit). By playing around with your data, I also discovered some inefficient data filtering code for long codon alignments and fixed it. HyPhy should load and filter the sequences about 10x faster for these types of data. Cheers, Sergei |
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