<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><div style="font-size: 14px; ">It's not an MPI requirement, just an execution error.</div><div style="font-size: 14px; "><br></div><div style="font-size: 14px; ">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.</div><div style="font-size: 14px; "><br></div><div style="font-size: 14px; ">Thanks,</div><div style="font-size: 14px; ">Carson</div><div style="font-size: 14px; "><br></div><div style="font-size: 14px; "><br></div><div style="font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family: Calibri; font-size: 11pt; text-align: left; color: black; border-bottom-width: medium; border-bottom-style: none; border-bottom-color: initial; border-left-width: medium; border-left-style: none; border-left-color: initial; padding-bottom: 0in; padding-left: 0in; padding-right: 0in; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; border-top-style: solid; border-right-width: medium; border-right-style: none; border-right-color: initial; padding-top: 3pt; "><span style="font-weight:bold">From: </span> Rob Syme <<a href="mailto:rob.syme@gmail.com">rob.syme@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Sunday, 26 May, 2013 10:26 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Can map2assembly be run outside the maker pipeline?<br></div><div style="font-size: 14px; "><br></div><div dir="ltr">Hi all<br><div style="font-size: 14px; "><br></div><div>I'm looking to move existing transcripts from one genome assembly to another, keeping the transcript names if possible. <div style="font-size: 14px; "><br></div><div style="font-size: 14px; ">Running map2assembly seems to require MPI (stderr example below). Is is possible to run map2assembly outside of the Maker pipeline and without MPI?</div><div style="font-size: 14px; "><br></div><div style="font-size: 14px; ">Stderr head:</div><div><span class="Apple-style-span" style="font-size: 12px;"><br></span></div><div><div><div><div><font face="courier new,monospace" style="font-size: 12px;">INFO: All repeat masking options will be skipped.</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><br></font></div><div><font face="courier new,monospace" style="font-size: 12px;">A data structure will be created for you at:</font></div><div><font face="courier new,monospace" style="font-size: 12px;">/path/to/maker/bin/SN15v2_scaffolds.maker.output/SN15v2_scaffolds_datastore</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><br></font></div><div><font face="courier new,monospace" style="font-size: 12px;">To access files for individual sequences use the datastore index:</font></div><div><font face="courier new,monospace" style="font-size: 12px;">/path/to/maker/bin/SN15v2_scaffolds.maker.output/SN15v2_scaffolds_master_datastore_index.log</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><br></font></div><div><font face="courier new,monospace" style="font-size: 12px;">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.</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><br></font></div><div><font face="courier new,monospace" style="font-size: 12px;">FATAL ERROR</font></div><div><font face="courier new,monospace" style="font-size: 12px;">ERROR: Failed in tier preparation</font></div><div><font face="courier new,monospace" style="font-size: 12px;">WARNING: You must always set a rank before running MpiTiers</font></div><div><font face="courier new,monospace" style="font-size: 12px;">FATAL: argument `q_def` does not exist in MpiTier object</font></div><div><font face="courier new,monospace" style="font-size: 12px;"> at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 86, <GEN10> line 1.</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x332dac8)', 'HASH(0x332db88)') called at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 47</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x2ef85a8)', 0, 0) called at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 413</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiChunk::__ANON__() called at /path/to/maker/bin/../lib/Error.pm line 415</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>eval {...} called at /path/to/maker/bin/../lib/Error.pm line 407</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Error::subs::try('CODE(0x2f49498)', 'HASH(0x332d728)') called at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 4165</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiChunk::_go('Process::MpiChunk=HASH(0x2f35e88)', 'load', 'HASH(0x2ef85a8)', 0, 0) called at /path/to/maker/bin/../lib/Process/MpiChunk.pm line 316</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>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</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiTiers::__ANON__() called at /path/to/maker/bin/../lib/Error.pm line 415</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>eval {...} called at /path/to/maker/bin/../lib/Error.pm line 407</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Error::subs::try('CODE(0x2f411a0)', 'HASH(0x2f491c8)') called at /path/to/maker/bin/../lib/Process/MpiTiers.pm line 375</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiTiers::_load_chunks('Process::MpiTiers=HASH(0x79f3d0)') called at /path/to/maker/bin/../lib/Process/MpiTiers.pm line 185</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiTiers::next_chunk('Process::MpiTiers=HASH(0x79f3d0)') called at /path/to/maker/bin/../lib/Process/MpiTiers.pm line 816</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>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</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiTiers::__ANON__('Error::Simple=HASH(0x2f35c18)', 'SCALAR(0x1179c30)') called at /path/to/maker/bin/../lib/Error.pm line 339</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>eval {...} called at /path/to/maker/bin/../lib/Error.pm line 329</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>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</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Error::subs::try('CODE(0x2f28898)', 'HASH(0x2f36230)') called at /path/to/maker/bin/../lib/Process/MpiTiers.pm line 79</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space:pre"> </span>Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x79f3d0)') called at /path/to/maker/bin/../lib/Process/MpiTiers.pm line 56</font></div><div><font face="courier new,monospace" style="font-size: 12px;"><span class="" style="white-space: pre; "> </span>Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x79f508)', 0, 'Process::MpiChunk') called at ./map2assembly line 205</font></div></div></div><div style="font-size: 14px; "><br></div></div></div></div>
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