[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

[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

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