<div><div>Hi everyone,</div><div><br></div><div>I ran maker2.25 without a problem, but with maker2.26, I encountered the following error after running it for ~8 hr with 2 nodes and 24 cpus, do you have any idea what's going on here? Some contigs did get finished, maybe this is not a big problem. My mpich2 version 1.4.1p1, job scheduling system is SGE. Thanks!</div>
<div><br></div><div>running  blast search.</div><div>#--------- command -------------#</div><div>Widget::blastx:</div><div>/home/yunfeiguo/Downloads/maker/bin/../exe/blast/bin/blastx -db /tmp/6480.1.all.q/maker_PQOTIq/concatPro%2Etxt.mpi.10.4 -query /tmp/6480.1.all.q/maker_PQOTIq/rank3/scaffold2602.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/7A/37/scaffold2602//theVoid.scaffold2602/scaffold2602.0.concatPro%2Etxt.blastx.temp_dir/concatPro%2Etxt.mpi.10.4.blastx</div>
<div>#-------------------------------#</div><div>deleted:-1 hits</div><div>SIGCHLD handler "DEFAULT" not defined.</div><div>SIGCHLD handler "DEFAULT" not defined.</div><div>running  exonerate search.</div>
<div>#--------- command -------------#</div><div>Widget::exonerate::protein2genome:</div><div>/home/username/usr/bin/exonerate -q /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/sp%7CQ8N8A2%7CANR44_HUMAN.for.1-3712.8.fasta -t /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/scaffold2590.1-3712.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/scaffold2590.1-3712.sp%7CQ8N8A2%7CANR44_HUMAN.p_exonerate.8</div>
<div>#-------------------------------#</div><div>Fatal error in MPI_Recv: Other MPI error, error stack:</div><div>MPI_Recv(186).............: MPI_Recv(buf=0x7fffa3a2e760, count=2, MPI_INT, src=MPI_ANY_SOURCE, tag=1111, MPI_COMM_WORLD, status=0x7fffa3a2e740) failed</div>
<div>dequeue_and_set_error(596): Communication error with rank 18</div><div>running  blast search.</div><div>#--------- command -------------#</div><div>Widget::blastx:</div><div>/home/yunfeiguo/Downloads/maker/bin/../exe/blast/bin/blastx -db /tmp/6480.1.all.q/maker_PQOTIq/concatPro%2Etxt.mpi.10.8 -query /tmp/6480.1.all.q/maker_PQOTIq/rank11/scaffold2575.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F0/AE/scaffold2575//theVoid.scaffold2575/scaffold2575.0.concatPro%2Etxt.blastx.temp_dir/concatPro%2Etxt.mpi.10.8.blastx</div>
<div>#-------------------------------#</div><div>running  blast search.</div><div>#--------- command -------------#</div><div>Widget::tblastx:</div><div>/home/yunfeiguo/Downloads/maker/bin/../exe/blast/bin/tblastx -db /tmp/6480.1.all.q/maker_PQOTIq/AllSebESTs_plus_Rubri%2Efasta.mpi.10.1 -query /tmp/6480.1.all.q/maker_PQOTIq/rank7/scaffold2620.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/6B/FB/scaffold2620//theVoid.scaffold2620/scaffold2620.0.AllSebESTs_plus_Rubri%2Efasta.tblastx.temp_dir/AllSebESTs_plus_Rubri%2Efasta.mpi.10.1.tblastx</div>
<div>#-------------------------------#</div><div>running  exonerate search.</div><div>#--------- command -------------#</div><div>Widget::exonerate::protein2genome:</div><div>/home/username/usr/bin/exonerate -q /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/sp%7CQ8NB46%7CANR52_HUMAN.for.1-3712.8.fasta -t /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/scaffold2590.1-3712.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/scaffold2590.1-3712.sp%7CQ8NB46%7CANR52_HUMAN.p_exonerate.8</div>
<div>#-------------------------------#</div><div>cleaning blastx...</div><div>in cluster::shadow_cluster...</div><div>...finished clustering.</div><div>cleaning clusters....</div><div>total clusters:1 now processing 0</div>
<div> ...processing 0 of 2</div><div>deleted:0 hits</div><div> ...processing 1 of 2</div><div>running  blast search.</div><div>#--------- command -------------#</div><div>Widget::tblastx:</div><div>/home/yunfeiguo/Downloads/maker/bin/../exe/blast/bin/tblastx -db /tmp/6480.1.all.q/maker_PQOTIq/AllSebESTs_plus_Rubri%2Efasta.mpi.10.6 -query /tmp/6480.1.all.q/maker_PQOTIq/rank9/scaffold2615.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/E2/6E/scaffold2615//theVoid.scaffold2615/scaffold2615.0.AllSebESTs_plus_Rubri%2Efasta.tblastx.temp_dir/AllSebESTs_plus_Rubri%2Efasta.mpi.10.6.tblastx</div>
<div>#-------------------------------#</div><div>deleted:0 hits</div><div>running  exonerate search.</div><div>#--------- command -------------#</div><div>Widget::exonerate::protein2genome:</div><div>/home/username/usr/bin/exonerate -q /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/tr%7CE7F7S0%7CE7F7S0_DANRE.for.1-3712.9.fasta -t /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/scaffold2590.1-3712.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /home/yunfeiguo/projects/fish/Nigro/run/dir_Nigro-53k00/Nigro-53k_part.maker.output/Nigro-53k_part_datastore/F9/9B/scaffold2590//theVoid.scaffold2590/<a href="http://scaffold2590.1-3712.tr">scaffold2590.1-3712.tr</a>%7CE7F7S0%7CE7F7S0_DANRE.p_exonerate.9</div>
<div>#-------------------------------#</div><div>deleted:0 hits</div><div>cleaning blastx...</div><div>cleaning clusters....</div><div>total clusters:1 now processing 0</div><div>cleaning clusters....</div><div>total clusters:1 now processing 0</div>
<div>deleted:-1 hits</div><div>deleted:-1 hits</div><div>deleted:-6 hits</div><div>deleted:-3 hits</div><div>deleted:-2 hits</div><div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>1 running and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div>
<div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre">        </span>1 running and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div>
<div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre">        </span>1 running and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div>
<div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div><div><span class="Apple-tab-span" style="white-space:pre">        </span>1 running and unjoined</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div><div>Perl exited with active threads:</div>
<div><span class="Apple-tab-span" style="white-space:pre">      </span>1 running and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>0 finished and unjoined</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>0 running and detached</div>
</div><div><br></div><div>Yunfei</div><div><br></div>