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

[Matt Simenc]

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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