<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">You probably have an error further upstream. The 'Argument "ALRM" isn't numeric’ error is just something you get as things are dieing in a non-elegant way, but the cause will be further up the error log.<div class=""><br class=""></div><div class="">The lack of fasta files means that you have no final gene models. Either your contigs are too short to produce a model, or your evidence alignments are insufficient in end-to-end coverage, splice site recovery on polishing, or %identity, so maker cannot elucidate a usable model from alignment alone.</div><div class=""><br class=""></div><div class="">What is your longest contig? Also try running GEGMA from the Korf lab, to help identify if the assembly is incomplete and by how much.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 10, 2014, at 6:42 AM, Jonathan Featherston <<a href="mailto:FeatherstonJ@arc.agric.za" class="">FeatherstonJ@arc.agric.za</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Dear Carson
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<div class="">I've been trying to train SNAP with Maker but I'm getting empty genome.ann and .dna files. I have tried running the maker2zff on the implant page to see if my script was corrupt. No help from that. I've seen a few pages in the group and on seqanswers about
the empty off files but most seem to have been resolved by including all outputs (maker2zff -n) and even this doesn't generate anything for me…. So I'm guessing the problem is somewhere with the maker outputs. </div>
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<div class="">I did get errors from the maker run but they seem to be about mli and ALRM (a perl error- what a pain getting perl libs on a mac).</div>
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<div class=""><font color="#0042aa" class="">Argument "ALRM" isn't numeric in exit at /Users/Jonathan/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/darwin-2level/forks.pm line 2184.</font></div>
<div class=""><font color="#0042aa" class="">Argument "ALRM" isn't numeric in exit at /Users/Jonathan/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/darwin-2level/forks.pm line 2184.</font></div>
<div class=""><font color="#0042aa" class="">Argument "ALRM" isn't numeric in exit at /Users/Jonathan/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/darwin-2level/forks.pm line 2184.</font></div>
<div class=""><font color="#0042aa" class="">Argument "ALRM" isn't numeric in exit at /Users/Jonathan/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/darwin-2level/forks.pm line 2184.</font></div>
<div class=""><font color="#0042aa" class="">Argument "ALRM" isn't numeric in exit at /Users/Jonathan/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/darwin-2level/forks.pm line 2184.</font></div>
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<div class=""><font color="#0042aa" class="">mpiexec has exited due to process rank 4 with PID 5935 on</font></div>
<div class=""><font color="#0042aa" class="">node Administrators-MacBook-Pro-9 exiting improperly. There are three reasons this could occur:</font></div>
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</font></div>
<div class=""><font color="#0042aa" class="">1. this process did not call "init" before exiting, but others in</font></div>
<div class=""><font color="#0042aa" class="">the job did. This can cause a job to hang indefinitely while it waits</font></div>
<div class=""><font color="#0042aa" class="">for all processes to call "init". By rule, if one process calls "init",</font></div>
<div class=""><font color="#0042aa" class="">then ALL processes must call "init" prior to termination.</font></div>
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</font></div>
<div class=""><font color="#0042aa" class="">2. this process called "init", but exited without calling "finalize".</font></div>
<div class=""><font color="#0042aa" class="">By rule, all processes that call "init" MUST call "finalize" prior to</font></div>
<div class=""><font color="#0042aa" class="">exiting or it will be considered an "abnormal termination"</font></div>
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</font></div>
<div class=""><font color="#0042aa" class="">3. this process called "MPI_Abort" or "orte_abort" and the mca parameter</font></div>
<div class=""><font color="#0042aa" class="">orte_create_session_dirs is set to false. In this case, the run-time cannot</font></div>
<div class=""><font color="#0042aa" class="">detect that the abort call was an abnormal termination. Hence, the only</font></div>
<div class=""><font color="#0042aa" class="">error message you will receive is this one.</font></div>
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</font></div>
<div class=""><font color="#0042aa" class="">This may have caused other processes in the application to be</font></div>
<div class=""><font color="#0042aa" class="">terminated by signals sent by mpiexec (as reported here).</font></div>
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</font></div>
<div class=""><font color="#0042aa" class="">You can avoid this message by specifying -quiet on the mpiexec command line. </font></div>
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<div class="">Maker did finish and the gff file produced (I can't produce a fasta file from the est2genome=1 option??) seems ok. It has produced protein-matches and match_part although I don't see maker product.</div>
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<div class="">Otherwise I ran maker with mli using the command from the CPBI maker paper. I used -nohup mpiexec -n 8 maker < /dev/null & for my maker execution. </div>
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<div class="">I'm using altest and protein homology for now. </div>
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<div class="">Thank you very much for what help you can provide. I really enjoyed the workshop you and Mark presented!</div>
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<div class="">Kind Regards</div>
<div class="">Jonathan</div>
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