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

[Fields, Christopher J]

Yup.  Though Bio-Root has been added back (which IIRC was the main problem with breakage on the master branch).

chris

> On Apr 19, 2016, at 10:19 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> FYI. BioPerl-live is not broken. Rather it is under active development and as such cannot be considered stable.
> 
> —Carson
> 
>> On Apr 19, 2016, at 9:18 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> 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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>> 
> 
> 
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