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<div>Hi Maker community,<br>
<br>
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.<br>
<b><br>
<br>
Error from first scaffold:</b><br>
------------- EXCEPTION: Bio::Root::Exception -------------<br>
MSG: no data for midline Sequence with id BL_ORD_ID:1562 no longer exists in database...alignment skipped<br>
STACK: Error::throw<br>
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<br>
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<br>
STACK: Widget::tblastx::keepers /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:114<br>
STACK: Widget::tblastx::parse /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:95<br>
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2676<br>
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2685<br>
STACK: Process::MpiChunk::_go /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:1858<br>
STACK: Process::MpiChunk::run /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:335<br>
STACK: main::node_thread /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/maker:1381<br>
STACK: threads::new /home/gkaur/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm:799<br>
STACK: /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/maker:864<br>
-----------------------------------------------------------<br>
--> rank=1, hostname=cn-r56<br>
--> rank=1, hostname=cn-r56<br>
--> rank=1, hostname=cn-r56<br>
--> rank=1, hostname=cn-r56<br>
ERROR: Failed while doing tblastx of alt-ESTs<br>
ERROR: Chunk failed at level:4, tier_type:2<br>
FAILED CONTIG:scaffold_52379<br>
<br>
ERROR: Chunk failed at level:5, tier_type:0<br>
FAILED CONTIG:scaffold_52379<br>
<br>
<br>
<b>Error from second scaffold:</b><br>
------------- EXCEPTION: Bio::Root::Exception -------------<br>
MSG: no data for midline Sequence with id BL_ORD_ID:3014 no longer exists in database...alignment skipped<br>
STACK: Error::throw<br>
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<br>
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<br>
STACK: Widget::tblastx::keepers /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:114<br>
STACK: Widget::tblastx::parse /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Widget/tblastx.pm:95<br>
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2676<br>
STACK: GI::tblastx_as_chunks /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/GI.pm:2685<br>
STACK: Process::MpiChunk::_go /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:1858<br>
STACK: Process::MpiChunk::run /home/gkaur/softwares/maker/maker-2.27_with_new_openmpi/bin/../lib/Process/MpiChunk.pm:335<br>
STACK: /home/softwares/maker/maker-2.27_with_new_openmpi/bin/maker:926<br>
-----------------------------------------------------------<br>
--> rank=1, hostname=cn-r12<br>
--> rank=1, hostname=cn-r12<br>
--> rank=1, hostname=cn-r12<br>
--> rank=1, hostname=cn-r12<br>
ERROR: Failed while doing tblastx of alt-ESTs<br>
ERROR: Chunk failed at level:4, tier_type:2<br>
FAILED CONTIG:scaffold_52359<br>
<br>
ERROR: Chunk failed at level:5, tier_type:0<br>
FAILED CONTIG:scaffold_52359<br>
<br>
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.<br>
Your help in understanding and resolving the error will be greatly appreciated.<br>
<br>
Thanks in advance,<br>
Gagan<br>
<br>
<div class="BodyFragment"><font size="2"><span style="font-size:10pt">
<div class="PlainText">- - - - - - - - - - - - - - - - -<br>
Gaganjot Kaur<br>
<br>
Bioinformatics Analyst<br>
The Centre for Applied Genomics (TCAG)<br>
The Hospital for Sick Children<br>
MaRS Building - East Tower<br>
101 College St., Room 14-701<br>
Toronto, ON M5G 1L7<br>
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