[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

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[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

[Kai Kamm]

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!

[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

[Carson Holt]

FYI. BioPerl-live is not broken. Rather it is under active development and as such cannot be considered stable.

—Carson

[Fields, Christopher J]

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

chris