<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Sorry for the slow reply. This got lost somehow. The file from the mailing list is 5 years old. Don’t use it. You are actually downgrading, not upgrading. You will break things.<div class=""><br class=""></div><div class="">Run maker outside of MPI (if you are using MPI). There might be additional error message, that are further back that are getting covered by extra MPI output. I don’t actually have a license for fgenesh to test with any more, so debugging it for you may be difficult. My guess is that a more recent version has slightly different output format which is breaking the parser. Also you need to restore the previous fgenesh.pm file before you can run any tests (may need to reinstall MAKER). </div><div class=""><br class=""></div><div class="">Also try MAKER3 vs MAKER2. They both run fgenesh slightly differently.</div><div class=""><br class=""></div><div class="">Basically after a couple of tests/error messages I may be able to send you something that would at least allow you to run fgenesh outside of MAKER to see what’s going on.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 7, 2019, at 12:43 PM, Kapeel Chougule <<a href="mailto:kapeelc@gmail.com" class="">kapeelc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi, Carson<div class=""><br class=""></div><div class="">I have been getting this error with fgenesh tool within MAKER. It runs ok with most of the assembly contigs but seems to fail on one contig or part of the contig with the below error</div><div class=""><br class=""></div><div class="">Widget::fgenesh:</div><div class="">/mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/bin/../lib/Widget/fgenesh/fgenesh_wrap /mnt/grid/ware/hpc_norepl/data/data/programs/fgenesh_v8/fgenesh_suite_v8.0.0a/fgenesh /sonas-hs/ware/hpc_norepl/data/programs/fgenesh_v8/fgenesh_suite_v8.0.0a/Zeamays.mpar.dat.new /tmp/uge/53139300.1.primary.q/maker_j3ttxX/6/6_1.600610-613023.Zeamays.mpar.dat.new.auto_annotator.fgenesh.fasta -exon_table:/tmp/uge/53139300.1.primary.q/maker_j3ttxX/6/6_1.600610-613023.Zeamays.mpar.dat.new.auto_annotator.xdef.fgenesh > /tmp/uge/53139300.1.primary.q/maker_j3ttxX/6/6_1.600610-613023.Zeamays.mpar.dat.new.auto_annotator.fgenesh</div><div class="">#-------------------------------#</div><div class=""> ...processing 9 of 24</div><div class=""> ...processing 8 of 28</div><div class=""> ...processing 10 of 24</div><div class=""> ...processing 9 of 28</div><div class=""> ...processing 11 of 24</div><div class=""> ...processing 10 of 28</div><div class=""> ...processing 12 of 24</div><div class=""> ...processing 11 of 28</div><div class="">deleted:0 genes</div><div class="">ERROR: FgenesH failed</div><div class="">--> rank=14, hostname=bnbcompute50</div><div class="">ERROR: Failed while annotating transcripts</div><div class="">ERROR: Chunk failed at level:1, tier_type:4</div><div class="">FAILED CONTIG:Super-Scaffold_14.2_contig2</div><div class=""><br class=""></div><div class="">I updated the perl module <a href="http://fgenesh.pm/" class="">fgenesh.pm</a> as suggested in the previous threads. Attached are the maker_opts.ctl and STDERR log file.</div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class="">Kapeel</div><div class=""><br class=""></div><div class=""> </div><div class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><font face="'courier new', monospace" class=""><b class=""><div class=""><br class=""></div><div class="">Kapeel Chougule<br class=""></div>Computational Scientist<font face="'courier new', monospace" class=""> Developer II<br class=""></font></b></font><font face="'courier new', monospace" class=""><b class=""><font face="'courier new', monospace" class="">One Bungtown Road Cold Spring Harbor, NY 11724<br class=""><font face="'courier new', monospace" class=""><a href="http://www.warelab.org/" target="_blank" class="">http://www.warelab.org/</a></font><br class=""><br class=""></font></b></font></div></div></div></div></div></div>
<span id="cid:f_jrv148nk0"><maker_opts.ctl></span><span id="cid:f_jrv148or1"><stderr.log></span>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></body></html>