<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="">A lock failure can become an issue if two separate jobs are running simultaneously. They may both try to process the same contig at the same time (modifying each others files) which will cause one or both to fail. On failure, it should always retry at some later point. So it can usually recover from this. If you see any partial lines in the resulting GFF3, then it did not recover and you need to just rerun whatever contig this happened on.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 18, 2016, at 12:14 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="">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.</div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, Nov 17, 2016 at 9:04 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">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).<div class=""><br class=""></div><div class="">The memory issue could be causing the lock failure as well.</div><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class="h5"><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Nov 17, 2016, at 7:53 PM, John Cornelius <<a href="mailto:jcornel3@asu.edu" target="_blank" class="">jcornel3@asu.edu</a>> wrote:</div><br class="m_4376896867475064397Apple-interchange-newline"><div class=""><div dir="ltr" class="">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:<div class=""><br class=""></div><div class="">ERROR: Lock broken in runlog<br class=""></div><div class=""><br class=""></div><div class="">With these lines found at the end:</div><div class=""><br class=""></div><div class=""><div class="">ERROR: Failed while polishig ESTs</div><div class="">ERROR: Chunk failed at level:2, tier_type:3</div><div class="">ERROR: Could not query process table: Cannot allocate memory at /packages/maker/2.31.8/bin/../<wbr class="">lib/Proc/ProcessTable_simple.<wbr class="">pm line 62.</div></div><div class=""><br class=""></div><div class="">From that last line it looks like the process is running out of RAM would that be right? Thanks.</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Nov 11, 2016 at 2:59 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" 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 class=""><blockquote type="cite" class=""><div class=""><div class="m_4376896867475064397h5"><div class="">On Nov 10, 2016, at 3:43 PM, John Cornelius <<a href="mailto:jcornel3@asu.edu" target="_blank" class="">jcornel3@asu.edu</a>> wrote:</div><br class="m_4376896867475064397m_-1631738957223432501Apple-interchange-newline"></div></div><div class=""><div class=""><div class="m_4376896867475064397h5"><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/<wbr class="">exonerate -q /tmp/maker_08Elxf/15/TRINITY_G<wbr class="">G_19079_c1670_g1_i1.for.847702<wbr class="">03-84771247.15.fasta -t /tmp/maker_08Elxf/15/chr9_10L.<wbr class="">84770203-84771247.15.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/maker_08Elxf/15/chr9_10L.<wbr class="">84770203-84771247.TRINITY_GG_1<wbr class="">9079_c1670_g1_i1.e.exonerate</div><div class="">#-----------------------------<wbr 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/<wbr class="">exonerate -q /tmp/maker_08Elxf/10/TRINITY_G<wbr class="">G_87963_c9694_g10_i12.for.4947<wbr class="">5083-49475985.10.fasta -t /tmp/maker_08Elxf/10/chr6L.494<wbr class="">75083-49475985.10.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/maker_08Elxf/10/chr6L.494<wbr class="">75083-49475985.TRINITY_GG_8796<wbr class="">3_c9694_g10_i12.e.exonerate</div><div class="">#-----------------------------<wbr class="">--#</div><div class=""><br class=""></div><div class="">==============================<wbr class="">==============================<wbr 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="">==============================<wbr class="">==============================<wbr 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" target="_blank" class="">jcornelius@tgen.org</a></div><div class="">#PBS -A tgen-205000</div><div class="">#PBS -o /scratch/jcornelius/xenopus_la<wbr class="">evis/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_la<wbr class="">evis/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="m_4376896867475064397m_-1631738957223432501gmail-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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______________________________<wbr class="">_________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" target="_blank" class="">maker-devel@box290.bluehost.co<wbr class="">m</a><br class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank" class="">http://box290.bluehost.com/mai<wbr class="">lman/listinfo/maker-devel_yand<wbr class="">ell-lab.org</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="m_4376896867475064397gmail_signature" data-smartmail="gmail_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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