[maker-devel] Updated Maker, having issues...

Thu Dec 26 08:08:30 MST 2013

Thanks so much for getting back to me! I did unpack the new version on top
of our old version by mistake, unfortunately. I re-installed both 2.28 and
2.30 without doing that again and both are giving me the same error. I
installed the BioPerl dependencies locally for Maker and it looks like it's
not automatically pointing to those when running. How can I tell Maker to
use the local dependencies? Do I need to bite the bullet and allow the
Build script to overwrite the BioPerl dependencies for the whole server?
There was a bit of an issue when I allowed Maker's Build to overwrite our
version of Augustus...

Here's the maker error:
$ maker
Can't locate MAKER/ConfigData.pm in @INC (@INC contains:
/home/usr/local/bin/../perl/lib /home/usr/local/bin/../lib
/home/usr/local/bin/../src/inc/perl/lib /usr/local/lib/perl5/5.8.8
/usr/local/lib/perl5/x86_64-linux-thread-multi /usr/local/lib/perl5
/usr/local/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/local/lib64/perl5/5.8.8 /usr/local/lib64/perl5
/usr/local/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/local/lib64/perl5/site_perl/5.8.8 /usr/local/lib64/perl5/site_perl
/usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl
/usr/local/pkg/eval/lib/perl5 /usr/local/pkg/glean-gene/lib
/usr/local/pkg/maker/lib
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at
/usr/local/bin/maker line 45.
BEGIN failed--compilation aborted at /usr/local/bin/maker line 45.

When I look for the missing module:
$ locate ConfigData.pm
/home/usr/local/lib/perl5/Bio/ConfigData.pm
/home/usr/local/lib/perl5/site_perl/5.8.8/Module/Build/ConfigData.pm
/home/usr/local/pkg/maker-2.28/perl/lib/MAKER/ConfigData.pm
/home/usr/local/pkg/maker-2.28/perl/lib/Module/Build/ConfigData.pm
/home/usr/local/pkg/maker-2.28/src/blib/lib/MAKER/ConfigData.pm
/home/usr/local/pkg/maker-2.28/src/inc/bundle/Module/Build/ConfigData.pm
/home/usr/local/pkg/maker-2.30p-beta/perl/lib/MAKER/ConfigData.pm
/home/usr/local/pkg/maker-2.30p-beta/perl/lib/Module/Build/ConfigData.pm
/home/usr/local/pkg/maker-2.30p-beta/src/blib/lib/MAKER/ConfigData.pm
/home/usr/local/pkg/maker-2.30p-beta/src/inc/bundle/Module/Build/ConfigData.pm
/home/usr/local/src/bioperl/bioperl-run/blib/lib/Bio/ConfigData.pm
/home/usr/local/src/bioperl/branch-1-6/blib/lib/Bio/ConfigData.pm
/home/usr/local/src/bioperl/core/blib/lib/Bio/ConfigData.pm
/usr/lib/perl5/vendor_perl/5.8.8/Module/Build/ConfigData.pm

On Fri, Dec 20, 2013 at 4:00 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I’d need the full error to tell you anything.  You can redirect STDERR to
> a file and attach it to an e-mail.  But a few gerneral things to check
> would be that your /tmp directory is not full, that you did not set TMP= in
> the maker_opt.ctl file to an NFS mounted location, and if you are using
> OpenMPI make sure you have set LD_PRELOAD to the appropriate value as
> required for use of OpenMPI’s shared libraries.
>
> Example —>
> export LD_PRELOAD=/usr/local/openmpi/lib/libmpi.so
>
> If LD_PRELOAD was the issue, you need to make sure it was set before even
> installing MAKER or it will not compile correctly (fresh reinstall required
> when this happens).
>
> Also make sure that when you were updating MAKER, you did not not unpack
> the new version tarball ontop of the old version of MAKER.  Binaries will
> not be updated through the unpack process, and will require you to
> reinstall from scratch.
>
> Thanks,
> Carson
>
>
> From: Emily Whiston <emwhist at gmail.com>
> Date: Tuesday, December 17, 2013 at 7:35 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Updated Maker, having issues...
>
> Hi,
> I updated our version of Maker today and I'm running into issues... I'm
> getting the following error message (it's LONG, so this is just the top
> bit):
>
> Process::MpiChunk::__ANON__() called at /usr/local/pkg/maker/lib/Error.pm
> line 415
> eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 407
> Error::subs::try(CODE(0x1f8c7430), HASH(0x1f955ed0)) called at
> /usr/local/pkg/maker/lib/Process/MpiChunk.pm line 4165
> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x1f8b4b80), "load",
> HASH(0x1f8b4960), 0, 0) called at
> /usr/local/pkg/maker/lib/Process/MpiChunk.pm line 316
> Process::MpiChunk::_loader(Process::MpiChunk=HASH(0x1f8b4b80),
> HASH(0x1f8b4960), 0, 0, Process::MpiTiers=HASH(0x1f8b47c0)) called at
> /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 364
> Process::MpiTiers::__ANON__() called at /usr/local/pkg/maker/lib/Error.pm
> line 415
> eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 407
> Error::subs::try(CODE(0x1f895dd0), HASH(0x1f8c7130)) called at
> /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 375
> Process::MpiTiers::_load_chunks(Process::MpiTiers=HASH(0x1f8b47c0)) called
> at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 185
> Process::MpiTiers::next_chunk(Process::MpiTiers=HASH(0x1f8b47c0)) called
> at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 816
> Process::MpiTiers::_handler(Process::MpiTiers=HASH(0x1f8b47c0),
> Error::Simple=HASH(0x1f895970), "Failed in tier preparation") called at
> /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 78
> Process::MpiTiers::__ANON__(Error::Simple=HASH(0x1f895970),
> SCALAR(0x1d6018c0)) called at /usr/local/pkg/maker/lib/Error.pm line 339
> eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 329
> Error::subs::run_clauses(HASH(0x1f91cbd0), "Can't call method
> \"get_Seq_by_id\" on an undefined value at /u"..., undef,
> ARRAY(0x1d614c50)) called at /usr/local/pkg/maker/lib/Error.pm line 426
> Error::subs::try(CODE(0x1f8c7480), HASH(0x1f91cbd0)) called at
> /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 79
> Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x1f8b47c0)) called at
> /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 56
> Process::MpiTiers::new("Process::MpiTiers", HASH(0x1cd3e520), 0,
> "Process::MpiChunk") called at /usr/local/bin/maker line 259
>
> FATAL ERROR
> ERROR: Failed while examining contents of the fasta file and run log
>
> FATAL ERROR
>
> FATAL ERROR
> ERROR: Can not load chunks
> WARNING: You must always set a rank before running MpiTiers
> FATAL: argument `out_dir` does not exist in MpiTier object
>
>
> I found another thread in the mailing list with the same error message and
> tried the advice there, but to no avail...
> http://gmod.827538.n3.nabble.com/Can-map2assembly-be-run-outside-the-maker-pipeline-tt4032901.html#a4032997
>
>
> I am running Maker with Snap and Augustus, using RNAseq-derived EST
> evidence and gene models from a close relative. Any advice would be much
> appreciated, as I'm rather desperate to get this up and running...
>
>
> Best,
>
> Emily
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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