[maker-devel] Maker Failed Contigs, Bio::Root::Exception

[Kai Kamm]

Hi,

while I have no problem running Maker on my desktop computer (Ubuntu 
14.04 LTS), I always get the error below (for all contigs) when I try to 
run Maker on a server.


------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not specify a Query End or Query Begin
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/homes/biertank/kai/bin/ActivePerl-5.20/site/lib/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::GenericHSP::_query_seq_feature 
/homes/biertank/kai/bin/ActivePerl-5.20/site/lib/Bio/Search/HSP/GenericHSP.pm:1525
STACK: Bio::Search::HSP::GenericHSP::query 
/homes/biertank/kai/bin/ActivePerl-5.20/site/lib/Bio/Search/HSP/GenericHSP.pm:956
STACK: Bio::Search::HSP::HSPI::start 
/homes/biertank/kai/bin/ActivePerl-5.20/site/lib/Bio/Search/HSP/HSPI.pm:504
STACK: PhatHit_utils::add_offset 
/homes/biertank/kai/maker/bin/../lib/PhatHit_utils.pm:1462
STACK: GI::parse_abinit_file /homes/biertank/kai/maker/bin/../lib/GI.pm:1199
STACK: Process::MpiChunk::_go 
/homes/biertank/kai/maker/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run 
/homes/biertank/kai/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: main::node_thread /homes/biertank/kai/maker/bin/maker:1454
STACK: threads::new 
/homes/biertank/kai/bin/ActivePerl-5.20/site/lib/forks.pm:799
STACK: /homes/biertank/kai/maker/bin/maker:914
-----------------------------------------------------------
--> rank=2, hostname=bioinf.uni-leipzig.de
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:scaffold20_cov246

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold20_cov246

examining contents of the fasta file and run log



I have tried to rerun "perl ./Build.PL" and then "./Build install" 
several times using different versions of Perl. To install the required 
Perl modules I have used "./Build installdeps" and I also tried 
installing the dependencies manually via CPAN - to no avail.

Any idea?

Thank you!
Kai