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

[Carson Holt]

Try updating BioPerl (use the CPAN version and not the BioPerl-live version because it will fail). Also use MAKER version 2.31.8 and not the 3.00.0-beta version.

Then make sure there is not error further up. What you are seeing may be a snowball effect of the real error which could be several screens back in the text. If you are using GFF3 files as input then your format is probably incorrect.

—Carson


> On Apr 18, 2016, at 7:13 AM, Kai Kamm <kai.kamm at ecolevol.de> wrote:
> 
> 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
> 
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