[maker-devel] Error running MAKER

[John Cornelius]

Would the lock failure cause problems with the annotation? It looks like
Maker is still progressing, just not as quickly as I thought it would be.

On Thu, Nov 17, 2016 at 9:04 PM, Carson Holt <carsonhh at gmail.com> wrote:

> To use less RAM, try lowering max_dna_len=, setting blast_depth=
> parameters to 20 pr 30 in maker_bopts.ctl (default is limitless), or when
> using MPI, starting fewer processes per node (requires manipulation of
> hostfile or using round robin distribution flag for MPI flavors where it is
> available).
>
> The memory issue could be causing the lock failure as well.
>
> —Carson
>
>
>
> On Nov 17, 2016, at 7:53 PM, John Cornelius <jcornel3 at asu.edu> wrote:
>
> Ok, so I went and searched one of the output logs for all the lines that
> say ERROR and I got 44 lines with the following message:
>
> ERROR: Lock broken in runlog
>
> With these lines found at the end:
>
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> ERROR: Could not query process table: Cannot allocate memory at
> /packages/maker/2.31.8/bin/../lib/Proc/ProcessTable_simple.pm line 62.
>
> From that last line it looks like the process is running out of RAM would
> that be right? Thanks.
>
> On Fri, Nov 11, 2016 at 2:59 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> 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_8796
>> 3_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
>> #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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>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
> --
> John Cornelius
> MCB PhD Candidate
> Arizona State University
>
>
>


-- 
John Cornelius
MCB PhD Candidate
Arizona State University
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