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

[Carson Holt]

I¹d 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 OpenMPI¹s 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-p
ipeline-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
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