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

[Rob Syme]

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_datastore_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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