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

[Carson Holt]

Intall as so —>
cpan> install Bio::Perl

But it sounds like you’ve got a proper version now. Most likely you had a non-cpan version of BioPerl installed. The version it gave met the ./Build dependency requirements, but it was really a broke version. This happens if you have BioPerl-live installed for example.

—Carson



> On Apr 19, 2016, at 6:36 AM, Kai Kamm <kai.kamm at ecolevol.de> wrote:
> 
> Hello,
> 
> now it seems to work. I (re)installed BioPerl like so:
> 
> ------------------------------------------------------------
> find the name of the latest BioPerl package:
> 
> cpan>d /bioperl/
> 
> ....
> 
> Distribution    CJFIELDS/BioPerl-1.6.901.tar.gz
> Distribution    CJFIELDS/BioPerl-1.6.922.tar.gz
> Distribution    CJFIELDS/BioPerl-1.6.924.tar.gz
> 
> And install the most recent:
> 
> cpan>install CJFIELDS/BioPerl-1.6.924.tar.gz
> ----------------------------------------------------------------
> 
> Produced some error messages during install, but Maker now works.
> 
> Just wonder why the BioPerl installation did not work properly with neither "./Build installdeps" nor via cpan>install Bundle::BioPerl.
> 
> And why it worked this way on my desktop.
> 
> Anyway
> Thanks!
> 
> 
> Am 18.04.2016 um 22:30 schrieb 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
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at yandell-lab.org
>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 
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