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

[Matt Simenc]

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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