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<p class="">Hi,</p><p class="">I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries.</p><p class="">I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP.</p><p class=""><b>Options I used include:</b><br></p><p class="">
</p><p class="">maker_gff=014_maker_Sacu_v1_s0008.gff</p><p class="">est_pass=1</p><p class="">altest_pass=0</p><p class="">protein_pass=1</p><p class="">rm_pass=1</p><p class="">model_pass=1</p><p class="">pred_pass=1</p><p class="">
</p><p class="">other_pass=0 </p><p class="">
</p><p class="">altest=alt_est.fasta</p><p class="">
</p><p class="">snaphmm=snap.hmm</p><p class="">
</p><p class="">trna=0</p><p class="">cpus=1</p><p class="">
</p><p class="">clean_try=0</p><p class="">
</p><p class="">clean_up=0</p><p class=""><br></p><p class=""><br></p><p class=""><b>Below are the last 50 lines in the stderr from the failed run.</b></p><p class=""><br></p><p class="">running blast search.</p>
<p class="">#--------- command -------------#</p>
<p class="">Widget::tblastx:</p>
<p class="">/share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -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/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx</p>
<p class="">#-------------------------------#</p>
<p class="">running blast search.</p>
<p class="">#--------- command -------------#</p>
<p class="">Widget::tblastx:</p>
<p class="">/share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -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/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx</p>
<p class="">#-------------------------------#</p>
<p class=""><br></p>
<p class="">------------- EXCEPTION: Bio::Root::Exception -------------</p>
<p class="">MSG: Can't get HSPs: data not collected.</p>
<p class="">STACK: Error::throw</p>
<p class="">STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449</p>
<p class="">STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552</p>
<p class="">STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/<a href="http://tblastx.pm:192">tblastx.pm:192</a></p>
<p class="">STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/<a href="http://tblastx.pm:133">tblastx.pm:133</a></p>
<p class="">STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952</p>
<p class="">STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961</p>
<p class="">STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469</p>
<p class="">STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289</p>
<p class="">STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361</p>
<p class="">STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341</p>
<p class="">STACK: /share/apps/genomics/maker/bin/maker:979</p>
<p class="">-----------------------------------------------------------</p>
<p class="">--> rank=31, hostname=kepler-0-8.local</p>
<p class="">--> rank=31, hostname=kepler-0-8.local</p>
<p class="">--> rank=31, hostname=kepler-0-8.local</p>
<p class="">--> rank=31, hostname=kepler-0-8.local</p>
<p class="">ERROR: Failed while collecting tblastx reports</p>
<p class="">ERROR: Chunk failed at level:5, tier_type:3</p>
<p class="">FAILED CONTIG:Sacu_v1_s0008</p>
<p class=""><br></p>
<p class="">ERROR: Chunk failed at level:4, tier_type:0</p>
<p class="">FAILED CONTIG:Sacu_v1_s0008</p>
<p class=""><br></p>
<p class="">examining contents of the fasta file and run log</p>
<p class=""><br></p><p class="">--Next Contig--</p><p class=""><br></p>
<p class="">Processing run.log file...</p>
<p class="">MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx</p>
<p class="">did not finish on the last run and must be erased</p><p class=""><br></p>
<p class="">Maker is now finished!!!</p>
<p class=""><br></p><p class=""><br></p><p class="">Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks!</p><p class="">Matt</p></div>