<div dir="ltr">Update:<div><br></div><div>So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. </div><div><br></div><div>However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features.</div><div><br></div><div>Thanks!</div><div>Matt</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc <span dir="ltr"><<a href="mailto:mcsimenc@gmail.com" target="_blank">mcsimenc@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<p>Hi,</p><p>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>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><b>Options I used include:</b><br></p><p>
</p><p>maker_gff=014_maker_Sacu_v1_s0008.gff</p><p>est_pass=1</p><p>altest_pass=0</p><p>protein_pass=1</p><p>rm_pass=1</p><p>model_pass=1</p><p>pred_pass=1</p><p>
</p><p>other_pass=0 </p><p>
</p><p>altest=alt_est.fasta</p><p>
</p><p>snaphmm=snap.hmm</p><p>
</p><p>trna=0</p><p>cpus=1</p><p>
</p><p>clean_try=0</p><p>
</p><p>clean_up=0</p><p><br></p><p><br></p><p><b>Below are the last 50 lines in the stderr from the failed run.</b></p><p><br></p><p>running blast search.</p>
<p>#--------- command -------------#</p>
<p>Widget::tblastx:</p>
<p>/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>#-------------------------------#</p>
<p>running blast search.</p>
<p>#--------- command -------------#</p>
<p>Widget::tblastx:</p>
<p>/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>#-------------------------------#</p>
<p><br></p>
<p>------------- EXCEPTION: Bio::Root::Exception -------------</p>
<p>MSG: Can't get HSPs: data not collected.</p>
<p>STACK: Error::throw</p>
<p>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>STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552</p>
<p>STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/<a href="http://tblastx.pm:192" target="_blank">tblastx.pm:192</a></p>
<p>STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/<a href="http://tblastx.pm:133" target="_blank">tblastx.pm:133</a></p>
<p>STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952</p>
<p>STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961</p>
<p>STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469</p>
<p>STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289</p>
<p>STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361</p>
<p>STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341</p>
<p>STACK: /share/apps/genomics/maker/bin/maker:979</p>
<p>-----------------------------------------------------------</p>
<p>--> rank=31, hostname=kepler-0-8.local</p>
<p>--> rank=31, hostname=kepler-0-8.local</p>
<p>--> rank=31, hostname=kepler-0-8.local</p>
<p>--> rank=31, hostname=kepler-0-8.local</p>
<p>ERROR: Failed while collecting tblastx reports</p>
<p>ERROR: Chunk failed at level:5, tier_type:3</p>
<p>FAILED CONTIG:Sacu_v1_s0008</p>
<p><br></p>
<p>ERROR: Chunk failed at level:4, tier_type:0</p>
<p>FAILED CONTIG:Sacu_v1_s0008</p>
<p><br></p>
<p>examining contents of the fasta file and run log</p>
<p><br></p><p>--Next Contig--</p><p><br></p>
<p>Processing run.log file...</p>
<p>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>did not finish on the last run and must be erased</p><p><br></p>
<p>Maker is now finished!!!</p>
<p><br></p><p><br></p><p>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><span class="HOEnZb"><font color="#888888"><p>Matt</p></font></span></div>
</blockquote></div><br></div>