<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I’m glad it’s working for you. Let us know if anything else comes up.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 20, 2017, at 6:34 AM, Vipul Patel <<a href="mailto:patel.kumar.vipul@gmail.com" class="">patel.kumar.vipul@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">Solved. After some digging and printing I found out the problem.<br class=""><br class="">It was snap itself!<br class=""><br class=""></div>For anybody who maybe runs in the same problem, check snap. Apparently it was not correctly compiled and therefore it produced a not conform output! Recompiling solved my issue. <br class=""><br class=""></div>Kind regards<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-01-20 9:44 GMT+01:00 Vipul Patel <span dir="ltr" class=""><<a href="mailto:patel.kumar.vipul@gmail.com" target="_blank" class="">patel.kumar.vipul@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class=""><div class="">Hi,<br class=""><br class=""></div>I hope someone can help me to figure out what is actually going wrong. <br class=""></div><div class=""><br class=""></div><div class="">I installed Maker 2.31.9, MPICH , BioPerl 1.7 via CPAN, pointed the TMP variable not to use NFS. The given testcase as well for 1k<small contigs < 1MB runs without any problems. <br class=""><br class=""></div><div class="">Applying it to a sequence, for example with 57MB it failes, I tried it as well with a different sequences around 60MB, same outcome. <br class=""><br class=""></div><div class="">I looked into the logs, but it was not really helpful as it was just stated that the job failed<br class=""></div><div class=""><br class=""></div><div class="">It crashed with following message:<br class=""><br class="">deleted:0 genes<br class="">substr outside of string at /usr/share/perl/5.18/Carp.pm line 165.<br class=""><br class="">------------- EXCEPTION: Bio::Root::Exception -------------<br class="">MSG: Calling translate without a seq argument!<br class="">STACK: Error::throw<br class="">STACK: Bio::Root::Root::throw /usr/local/share/perl/5.18.2/<wbr class="">Bio/Root/Root.pm:447<br class="">STACK: Bio::Tools::CodonTable::<wbr class="">translate /usr/local/share/perl/5.18.2/<wbr class="">Bio/Tools/CodonTable.pm:419<br class="">STACK: CGL::TranslationMachine::<wbr class="">longest_translation_plus_stop programs/maker/maker/bin/../<wbr class="">lib/CGL/TranslationMachine.pm:<wbr class="">280<br class="">STACK: maker::auto_annotator::get_<wbr class="">translation_seq programs/maker/maker/bin/../<wbr class="">lib/maker/<a href="http://auto_annotator.pm:3236/" target="_blank" class="">auto_annotator.pm:<wbr class="">3236</a><br class="">STACK: Widget::snap::load_phat_hits programs/maker/maker/bin/../<wbr class="">lib/Widget/<a href="http://snap.pm:974/" target="_blank" class="">snap.pm:974</a><br class="">STACK: Widget::snap::parse programs/maker/maker/bin/../<wbr class="">lib/Widget/<a href="http://snap.pm:690/" target="_blank" class="">snap.pm:690</a><br class="">STACK: GI::parse_abinit_file programs/maker/maker/bin/../<wbr class="">lib/GI.pm:1194<br class="">STACK: Process::MpiChunk::_go programs/maker/maker/bin/../<wbr class="">lib/Process/MpiChunk.pm:1469<br class="">STACK: Process::MpiChunk::run programs/maker/maker/bin/../<wbr class="">lib/Process/MpiChunk.pm:341<br class="">STACK: programs/maker/maker/bin/<wbr class="">maker:979<br class="">------------------------------<wbr class="">-----------------------------<br class="">--> rank=16, hostname=dummy<br class="">ERROR: Failed while gathering ab-init output files<br class="">ERROR: Chunk failed at level:1, tier_type:2<br class="">FAILED CONTIG:chr_test<br class=""><br class="">ERROR: Chunk failed at level:4, tier_type:0<br class="">FAILED CONTIG:chr_test<br class=""><br class="">examining contents of the fasta file and run log<br class=""><br class=""><br class=""><br class="">--Next Contig--<br class=""><br class="">Processing run.log file...<br class=""><br class=""></div><div class="">I got the same message if I run it without MPI, So I can guess it is not an MPI issue. <br class=""></div><div class="">How can I find out if some jobs died so maybe this could lead to this problem?<br class=""></div><div class="">Other ideas how I can tackle this problem?<br class=""><br class=""></div><div class="">Kind regards<br class=""></div></div>
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