[maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully
Carson Holt
carsonhh at gmail.com
Mon Jul 18 08:55:29 MDT 2016
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.
Thanks,
Carson
> On Jul 15, 2016, at 9:20 PM, Matt Simenc <mcsimenc at gmail.com> wrote:
>
> 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?
>
> On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc <mcsimenc at gmail.com <mailto:mcsimenc at gmail.com>> wrote:
> Hi,
>
> 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.
>
> 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.
>
> Options I used include:
>
>
> maker_gff=014_maker_Sacu_v1_s0008.gff
>
> est_pass=1
>
> altest_pass=0
>
> protein_pass=1
>
> rm_pass=1
>
> model_pass=1
>
> pred_pass=1
>
>
> other_pass=0
>
>
> altest=alt_est.fasta
>
>
> snaphmm=snap.hmm
>
>
> trna=0
>
> cpus=1
>
>
> clean_try=0
>
>
> clean_up=0
>
>
>
>
>
> Below are the last 50 lines in the stderr from the failed run.
>
>
>
> running blast search.
>
> #--------- command -------------#
>
> Widget::tblastx:
>
> /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
>
> #-------------------------------#
>
> running blast search.
>
> #--------- command -------------#
>
> Widget::tblastx:
>
> /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
>
> #-------------------------------#
>
>
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
>
> MSG: Can't get HSPs: data not collected.
>
> STACK: Error::throw
>
> STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449
>
> STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552
>
> STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 <http://tblastx.pm:192/>
> STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 <http://tblastx.pm:133/>
> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952
>
> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961
>
> STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469
>
> STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289
>
> STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361
>
> STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341
>
> STACK: /share/apps/genomics/maker/bin/maker:979
>
> -----------------------------------------------------------
>
> --> rank=31, hostname=kepler-0-8.local
>
> --> rank=31, hostname=kepler-0-8.local
>
> --> rank=31, hostname=kepler-0-8.local
>
> --> rank=31, hostname=kepler-0-8.local
>
> ERROR: Failed while collecting tblastx reports
>
> ERROR: Chunk failed at level:5, tier_type:3
>
> FAILED CONTIG:Sacu_v1_s0008
>
>
>
> ERROR: Chunk failed at level:4, tier_type:0
>
> FAILED CONTIG:Sacu_v1_s0008
>
>
>
> examining contents of the fasta file and run log
>
>
>
> --Next Contig--
>
>
>
> Processing run.log file...
>
> 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
>
> did not finish on the last run and must be erased
>
>
>
> Maker is now finished!!!
>
>
>
>
>
> 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!
>
> Matt
>
>
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