Dear Jan, > I've run into a weird problem with seqret after downloading the complete > protein refseq database and indexing that with dbxflat. The problem > seems to be triggered by a rare condition, so far I've only encountered > it with accession ZP_10312765: > > % seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 > > Monitoring the seqret process using top, I noticed that the process > grows to a size of 2g before segfaulting. > > Trying the same with ZP_10312766, the next record in the file, causes > no problem. Also, -osformat=fasta and -osformat=genbank work with > ZP_10312765, so the problem seems to be with outputting the swiss format.
I can reproduce the problem with the latest EMBOSS. The problem seems to be trying to wrap a feature line to 41 bytes per record when the coded_by location is longer than the available width. I will work on a patch for the latest release and also for the 6.4 release you were using. Many thanks for finding this one. Peter Rice EMBOSS Team _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
