[maker-devel] Can map2assembly be run outside the maker pipeline?

[Carson Holt]

It's not an MPI requirement, just an execution error.

I've attached a fixed version of that script.  Really it is just a wrapper
that runs maker with a few parameters changes.  You can do the exact same
thing by removing all repeat mask options, setting est2genome=1 and then an
adding est_forward=1 to the maker_opts.ctl file.

Thanks,
Carson



From:  Rob Syme <rob.syme at gmail.com>
Date:  Sunday, 26 May, 2013 10:26 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Can map2assembly be run outside the maker pipeline?

Hi all

I'm looking to move existing transcripts from one genome assembly to
another, keeping the transcript names if possible.

Running map2assembly seems to require MPI (stderr example below). Is is
possible to run map2assembly outside of the Maker pipeline and without MPI?

Stderr head:

INFO: All repeat masking options will be skipped.

A data structure will be created for you at:
/path/to/maker/bin/SN15v2_scaffolds.maker.output/SN15v2_scaffolds_datastore

To access files for individual sequences use the datastore index:
/path/to/maker/bin/SN15v2_scaffolds.maker.output/SN15v2_scaffolds_master_dat
astore_index.log

Can't call method "get_Seq_by_id" on an undefined value at
/path/to/maker/bin/../lib/Process/MpiChunk.pm line 226, <GEN10> line 1.

FATAL ERROR
ERROR: Failed in tier preparation
WARNING: You must always set a rank before running MpiTiers
FATAL: argument `q_def` does not exist in MpiTier object
 at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 86, <GEN10> line 1.
Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x332dac8)',
'HASH(0x332db88)') called at /path/to/maker/bin/../lib/Process/MpiChunk.pm
line 47
Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x2ef85a8)', 0, 0) called
at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 413
Process::MpiChunk::__ANON__() called at /path/to/maker/bin/../lib/Error.pm
line 415
eval {...} called at /path/to/maker/bin/../lib/Error.pm line 407
Error::subs::try('CODE(0x2f49498)', 'HASH(0x332d728)') called at
/path/to/maker/bin/../lib/Process/MpiChunk.pm line 4165
Process::MpiChunk::_go('Process::MpiChunk=HASH(0x2f35e88)', 'load',
'HASH(0x2ef85a8)', 0, 0) called at
/path/to/maker/bin/../lib/Process/MpiChunk.pm line 316
Process::MpiChunk::_loader('Process::MpiChunk=HASH(0x2f35e88)',
'HASH(0x2ef85a8)', 0, 0, 'Process::MpiTiers=HASH(0x79f3d0)') called at
/path/to/maker/bin/../lib/Process/MpiTiers.pm line 364
Process::MpiTiers::__ANON__() called at /path/to/maker/bin/../lib/Error.pm
line 415
eval {...} called at /path/to/maker/bin/../lib/Error.pm line 407
Error::subs::try('CODE(0x2f411a0)', 'HASH(0x2f491c8)') called at
/path/to/maker/bin/../lib/Process/MpiTiers.pm line 375
Process::MpiTiers::_load_chunks('Process::MpiTiers=HASH(0x79f3d0)') called
at /path/to/maker/bin/../lib/Process/MpiTiers.pm line 185
Process::MpiTiers::next_chunk('Process::MpiTiers=HASH(0x79f3d0)') called at
/path/to/maker/bin/../lib/Process/MpiTiers.pm line 816
Process::MpiTiers::_handler('Process::MpiTiers=HASH(0x79f3d0)',
'Error::Simple=HASH(0x2f35c18)', 'Failed in tier preparation') called at
/path/to/maker/bin/../lib/Process/MpiTiers.pm line 78
Process::MpiTiers::__ANON__('Error::Simple=HASH(0x2f35c18)',
'SCALAR(0x1179c30)') called at /path/to/maker/bin/../lib/Error.pm line 339
eval {...} called at /path/to/maker/bin/../lib/Error.pm line 329
Error::subs::run_clauses('HASH(0x2f36230)', 'Can\'t call method
"get_Seq_by_id" on an undefined value at /...', undef, 'ARRAY(0x117a1e8)')
called at /path/to/maker/bin/../lib/Error.pm line 426
Error::subs::try('CODE(0x2f28898)', 'HASH(0x2f36230)') called at
/path/to/maker/bin/../lib/Process/MpiTiers.pm line 79
Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x79f3d0)') called at
/path/to/maker/bin/../lib/Process/MpiTiers.pm line 56
Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x79f508)', 0,
'Process::MpiChunk') called at ./map2assembly line 205

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