[maker-devel] Error running MAKER

[Carson Holt]

The cause of the error is probably further back in the STDERR. With MPI so many processes are producing status and notes, that you can get several seconds of output after ta failure. If you kept the whole STDERR, I can help you look through it.  searching for “ERROR” all caps is usually where you will see it. Also MAKER keeps a log of progress, so even on failure, you can just restart it and it will pick up the analysis from the last successful step.

—Carson


> On Nov 10, 2016, at 3:43 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
> Hello, I'm using MAKER to annotate a tetraploid genome and while running it, I encountered the following error:
> 
> #--------- command -------------#
> Widget::exonerate::est2genome:
> /packages/exonerate-2.2.0/bin/exonerate  -q /tmp/maker_08Elxf/15/TRINITY_GG_19079_c1670_g1_i1.for.84770203-84771247.15.fasta -t /tmp/maker_08Elxf/15/chr9_10L.84770203-84771247.15.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/maker_08Elxf/15/chr9_10L.84770203-84771247.TRINITY_GG_19079_c1670_g1_i1.e.exonerate
> #-------------------------------#
> running  est2genome search.
> #--------- command -------------#
> Widget::exonerate::est2genome:
> /packages/exonerate-2.2.0/bin/exonerate  -q /tmp/maker_08Elxf/10/TRINITY_GG_87963_c9694_g10_i12.for.49475083-49475985.10.fasta -t /tmp/maker_08Elxf/10/chr6L.49475083-49475985.10.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/maker_08Elxf/10/chr6L.49475083-49475985.TRINITY_GG_87963_c9694_g10_i12.e.exonerate
> #-------------------------------#
> 
> ===================================================================================
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 132376 RUNNING AT pnap-pe7-s03
> =   EXIT CODE: 135
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Bus error (signal 7)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
> 
> The the command I ran was the following:
> 
> #PBS -l walltime=240:00:00
> #PBS -N MAKER
> #PBS -l nodes=1:ppn=16
> ##PBS -q hmem
> #PBS -j oe
> #PBS -m abe
> #PBS -M jcornelius at tgen.org <mailto:jcornelius at tgen.org>
> #PBS -A tgen-205000
> #PBS -o /scratch/jcornelius/xenopus_laevis/maker_run
> 
> # --- load required modules --- #
> 
> module load maker
> 
> # --- run maker --- #
> 
> cd /scratch/jcornelius/xenopus_laevis/maker_run
> mpiexec -n 16 maker -base XLNEURO.run1 -fix_nucleotides
> 
> I'm not sure what could be causing this error and any help would be much appreciated. Thanks.
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
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