[maker-devel] Maker error: failed while doing tblastx of alt-ESTs

[Gaganjot Kaur]

Hi Maker community,

I have been trying to annotate a fungal genome using maker. As I do not have ests from the same species I have been using proteins and ests from two related species. Maker finishes successfully for all the scaffolds except two. These two scaffolds are around 2 mega bases each. I am running maker-2.27, using mpiexec to run over multiple compute nodes . Please see the error log below.


Error from first scaffold:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: no data for midline Sequence with id BL_ORD_ID:1562 no longer exists in database...alignment skipped
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/gkaur/tools/CentOS6/perl/5.14.2-usethreads/lib/site_perl/5.14.2/Bio/Root/Root.pm:472
STACK: Bio::SearchIO::blast::next_result /home/gkaur/tools/CentOS6/perl/5.14.2-usethreads/lib/site_perl/5.14.2/Bio/SearchIO/blast.pm:1888
STACK: Widget::tblastx::keepers /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:114
STACK: Widget::tblastx::parse /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:95
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2676
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2685
STACK: Process::MpiChunk::_go /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:1858
STACK: Process::MpiChunk::run /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:335
STACK: main::node_thread /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/maker:1381
STACK: threads::new /home/gkaur/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm:799
STACK: /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/maker:864
-----------------------------------------------------------
--> rank=1, hostname=cn-r56
--> rank=1, hostname=cn-r56
--> rank=1, hostname=cn-r56
--> rank=1, hostname=cn-r56
ERROR: Failed while doing tblastx of alt-ESTs
ERROR: Chunk failed at level:4, tier_type:2
FAILED CONTIG:scaffold_52379

ERROR: Chunk failed at level:5, tier_type:0
FAILED CONTIG:scaffold_52379


Error from second scaffold:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: no data for midline Sequence with id BL_ORD_ID:3014 no longer exists in database...alignment skipped
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/gkaur/tools/CentOS6/perl/5.14.2-usethreads/lib/site_perl/5.14.2/Bio/Root/Root.pm:472
STACK: Bio::SearchIO::blast::next_result /home/gkaur/tools/CentOS6/perl/5.14.2-usethreads/lib/site_perl/5.14.2/Bio/SearchIO/blast.pm:1888
STACK: Widget::tblastx::keepers /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:114
STACK: Widget::tblastx::parse /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:95
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2676
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2685
STACK: Process::MpiChunk::_go /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:1858
STACK: Process::MpiChunk::run /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:335
STACK: /home/softwares/maker/maker-2.27_with_new_openmpi/bin/maker:926
-----------------------------------------------------------
--> rank=1, hostname=cn-r12
--> rank=1, hostname=cn-r12
--> rank=1, hostname=cn-r12
--> rank=1, hostname=cn-r12
ERROR: Failed while doing tblastx of alt-ESTs
ERROR: Chunk failed at level:4, tier_type:2
FAILED CONTIG:scaffold_52359

ERROR: Chunk failed at level:5, tier_type:0
FAILED CONTIG:scaffold_52359

The errors seem to come from alt-est that I have been using. I have tried running maker more than once over these two scaffolds and the same error appears each time. I have no idea what is going wrong here.
Your help in understanding and resolving the error will be greatly appreciated.

Thanks in advance,
Gagan

- - - - - - - - - - - - - - - - -
Gaganjot Kaur

Bioinformatics Analyst
The Centre for Applied Genomics (TCAG)
The Hospital for Sick Children
MaRS Building - East Tower
101 College St., Room 14-701
Toronto, ON M5G 1L7

________________________________

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130529/31a19cee/attachment-0002.html>