<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk. This will cause IO errors and partial result files because the operations done in TMP are not NFS safe.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson </div><div class=""><br class=""></div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On Jul 15, 2016, at 9:20 PM, Matt Simenc <<a href="mailto:mcsimenc@gmail.com" class="">mcsimenc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas?<br class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc <span dir="ltr" class=""><<a href="mailto:mcsimenc@gmail.com" target="_blank" class="">mcsimenc@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 dir="ltr" class=""><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 class="">Options I used include:</b><br class=""></p><div class="">
<br class="webkit-block-placeholder"></div><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><div class="">
<br class="webkit-block-placeholder"></div><p class="">other_pass=0 </p><div class="">
<br class="webkit-block-placeholder"></div><p class="">altest=alt_est.fasta</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">snaphmm=snap.hmm</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">trna=0</p><p class="">cpus=1</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">clean_try=0</p><div class="">
<br class="webkit-block-placeholder"></div><p class="">clean_up=0</p><p class=""><br class=""></p><p class=""><br class=""></p><p class=""><b class="">Below are the last 50 lines in the stderr from the failed run.</b></p><p class=""><br 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="">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 class=""></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/" target="_blank" class="">tblastx.pm:192</a></p><p class="">STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/<a href="http://tblastx.pm:133/" target="_blank" class="">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 class=""></p><p class="">ERROR: Chunk failed at level:4, tier_type:0</p><p class="">FAILED CONTIG:Sacu_v1_s0008</p><p class=""><br class=""></p><p class="">examining contents of the fasta file and run log</p><p class=""><br class=""></p><p class="">--Next Contig--</p><p class=""><br class=""></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 class=""></p><p class="">Maker is now finished!!!</p><p class=""><br class=""></p><p class=""><br class=""></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><span class="HOEnZb"><font color="#888888" class=""><p class="">Matt</p></font></span></div>
</blockquote></div><br class=""></div></div>
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