[maker-devel] Maker

[Carson Holt]

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.

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.

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.

—Carson



> On Nov 10, 2014, at 6:42 AM, Jonathan Featherston <FeatherstonJ at arc.agric.za> wrote:
> 
> Dear Carson
> 
> 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. 
> 
> 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).
> 
> 
> 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.
> 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.
> 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.
> 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.
> 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.
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 4 with PID 5935 on
> node Administrators-MacBook-Pro-9 exiting improperly. There are three reasons this could occur:
> 
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
> 
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
> 
> 3. this process called "MPI_Abort" or "orte_abort" and the mca parameter
> orte_create_session_dirs is set to false. In this case, the run-time cannot
> detect that the abort call was an abnormal termination. Hence, the only
> error message you will receive is this one.
> 
> This may have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> 
> You can avoid this message by specifying -quiet on the mpiexec command line. 
> 
> 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.
> 
> 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. 
> 
> I'm using altest  and protein homology for now. 
> 
> Thank you very much for what help you can provide. I really enjoyed the workshop you and Mark presented!
> 
> Kind Regards
> Jonathan
> 
> 
> 
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