Dear all,

I'm experiencing very weird problem trying to launch standalone polyphen2.

During run_pph.pm launch on input file with about 1000 lines, describing protein variants, fail occurs: after approx. 400 lines being successfully parsed, blastdbcmd starts to fail randomly with 255 error code (Unknown error, according to blastdbcmd manual) on protein sequences extraction step, performed by PPH.pm -> PPH/Seq.pm -> fastacmd.

It could look like there is no protein with such ID in db, but when i retrieve this ID separately, by command as written below, it returns successfully.

bin/blastdbcmd -db uniprot/human -dbtype prot -entry P20062 -out ~/tmp.f -outfmt %f

So I have no idea, what could go wrong. Free disk space for temp files is more than enough, and Google'ing does not help at all. Did anyone encountered problem like this?