[maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully

Mon Jul 18 09:20:34 MDT 2016

Oops! I meant to reply to a different thread, not this one. That last
message is related to a different problem.

On Mon, Jul 18, 2016 at 8:18 AM, Matt Simenc <mcsimenc at gmail.com> wrote:

> Update:
>
> So I isolated a single scaffold to run MAKER on and test different
> parameters. With map_forward=1 the duplicates disappeared.
>
> 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.
>
> Thanks!
> Matt
>
> On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc <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
>>
>> STACK: Widget::tblastx::parse
>> /share/apps/genomics/maker/bin/../lib/Widget/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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