<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 10, 2016, at 3:43 PM, John Cornelius <<a href="mailto:jcornel3@asu.edu" class="">jcornel3@asu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello, I'm using MAKER to annotate a tetraploid genome and while running it, I encountered the following error:<br class=""><br class=""><div class="">#--------- command -------------#</div><div class="">Widget::exonerate::est2genome:</div><div class="">/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</div><div class="">#-------------------------------#</div><div class="">running est2genome search.</div><div class="">#--------- command -------------#</div><div class="">Widget::exonerate::est2genome:</div><div class="">/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</div><div class="">#-------------------------------#</div><div class=""><br class=""></div><div class="">===================================================================================</div><div class="">= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</div><div class="">= PID 132376 RUNNING AT pnap-pe7-s03</div><div class="">= EXIT CODE: 135</div><div class="">= CLEANING UP REMAINING PROCESSES</div><div class="">= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</div><div class="">===================================================================================</div><div class="">YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Bus error (signal 7)</div><div class="">This typically refers to a problem with your application.</div><div class="">Please see the FAQ page for debugging suggestions</div><div class=""><br class=""></div><div class="">The the command I ran was the following:</div><div class=""><br class=""></div><div class=""><div class="">#PBS -l walltime=240:00:00</div><div class="">#PBS -N MAKER</div><div class="">#PBS -l nodes=1:ppn=16</div><div class="">##PBS -q hmem</div><div class="">#PBS -j oe</div><div class="">#PBS -m abe</div><div class="">#PBS -M <a href="mailto:jcornelius@tgen.org" class="">jcornelius@tgen.org</a></div><div class="">#PBS -A tgen-205000</div><div class="">#PBS -o /scratch/jcornelius/xenopus_laevis/maker_run</div><div class=""><br class=""></div><div class=""># --- load required modules --- #</div><div class=""><br class=""></div><div class="">module load maker</div><div class=""><br class=""></div><div class=""># --- run maker --- #</div><div class=""><br class=""></div><div class="">cd /scratch/jcornelius/xenopus_laevis/maker_run</div><div class="">mpiexec -n 16 maker -base XLNEURO.run1 -fix_nucleotides</div></div><div class=""><br class=""></div><div class="">I'm not sure what could be causing this error and any help would be much appreciated. Thanks.</div>-- <br class=""><div class="gmail-m_-6154802559924617561gmail_signature"><div dir="ltr" class="">John Cornelius<br class="">MCB PhD Candidate<br class="">Arizona State University<br class=""></div></div>
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