I think I hit this bug already but did not report it. It came now through a maker-devel email list and provided 0.360.0 version was released 27 Jun 2014 it should be still relevant issue for my current perl-5.20.1 install. From Carson Holt Subject: Re: [maker-devel] Segmentation Fault Date: Thu, 30 Jun 2016 12:11:31 -0600 ... Finally the error from the forks module. See the following from the devel list —> https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version) —Carson > On Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <mmacd@udel.edu> wrote: > > Hi Maker, > I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds. > > sh: line 1: 34865 Segmentation fault (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate > Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm line 1736. > Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm line 1736. > ERROR: Exonerate failed > --> rank=1, hostname=biomix2.dbi.local > ERROR: Failed while polishing proteins > ERROR: Chunk failed at level:10, tier_type:3 > FAILED CONTIG:picr50 > ... > _______________________________________________ > maker-devel mailing list > maker-devel@box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org BTW, I do not see it even reported in https://rt.cpan.org/Public/Dist/Display.html?Name=forks . Anybody haviong time to report there? ;) Thank you.
Tests of forks pass here (with 5.24.1-rc4); is this still a problem?
Do not know, I was hoping somebody checks the old patch content and whatever is the current version. ;)
(In reply to Martin Mokrejš from comment #2) > Do not know, I was hoping somebody checks the old patch content and whatever > is the current version. ;) OK let's assume it is fixed...
