<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-size: 14px; font-family: Calibri, sans-serif;"><div>Could you make sure trna=0 is set in the maker_opt.ctl file, and leave that off for the time being. It is a new feature that was added since 2.28, and may be a little buggy. I’ll try and replicate the error here. Could you send me a copy of your maker_opts.ctl file. For the mean time just turn off the trna option and you should be able to run, you can always run with trna=1 later (even by itself as a separate run) without loosing anything.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> carlos vargas <<a href="mailto:charlos9@gmail.com">charlos9@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, January 22, 2014 at 5:34 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Problem before running ab-initio predictors<br></div><div><br></div><div dir="ltr">Hello,<div><br></div><div>I finally was able to install maker with mpi support, however now I see a new error which I wasn't seeing before. Both for mpiexec and single maker runs I observe the following error just after it finishes running exonerate. </div><div><br></div><div><br></div><div>Thank you for your time!</div><div><br></div><div>Carlos</div><div><br><div><div>deleted:0 hits</div><div>collecting blastx reports</div><div>flattening protein clusters</div><div>prepare section files</div><div>processing the chunk divide</div><div>preparing evidence clusters for annotations</div><div>Preparing evidence for hint based annotation</div><div>cleaning clusters....</div><div>total clusters:1 now processing 0</div><div>cleaning clusters....</div><div>total clusters:1 now processing 0</div><div>annotating transcripts</div><div>Making transcripts</div><div> ...processing 0 of 1</div><div>ERROR: Not a valid predictor in auto_annoator::get_pred_shot</div><div> at /home/cvargas/maker/bin/../lib/maker/<a href="http://auto_annotator.pm">auto_annotator.pm</a> line 2155.</div><div><span class="" style="white-space:pre"> </span>maker::auto_annotator::get_pred_shot(FastaSeq=HASH(0x3eb6920), ">2973", "/gnmP05/Carlos/mpiannotatetest/longest.maker.output/longest_d"..., undef, HASH(0x3eeb9f8), 0, "trnascan", HASH(0x3fb1f80), runlog=HASH(0x3ec6e38), ...) called at /home/cvargas/maker/bin/../lib/maker/<a href="http://auto_annotator.pm">auto_annotator.pm</a> line 1923</div><div><span class="" style="white-space:pre"> </span>maker::auto_annotator::run_it(ARRAY(0x3fab4d0), "/gnmP05/Carlos/mpiannotatetest/longest.maker.output/longest_d"..., FastaSeq=HASH(0x3eb6920), FastaSeq=HASH(0x3ed42d0), ">2973", "trnascan", HASH(0x3fb1f80)) called at /home/cvargas/maker/bin/../lib/maker/<a href="http://auto_annotator.pm">auto_annotator.pm</a> line 920</div><div><span class="" style="white-space:pre"> </span>maker::auto_annotator::annotate_trans(FastaSeq=HASH(0x3ed42d0), FastaSeq=HASH(0x3eb6920), ">2973", 2973, ARRAY(0x3e818f8), "/gnmP05/Carlos/mpiannotatetest/longest.maker.output/longest_d"..., HASH(0x3fb1f80), runlog=HASH(0x3ec6e38)) called at /home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 3775</div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::__ANON__() called at /home/cvargas/maker/bin/../lib/Error.pm line 415</div><div><span class="" style="white-space:pre"> </span>eval {...} called at /home/cvargas/maker/bin/../lib/Error.pm line 407</div><div><span class="" style="white-space:pre"> </span>Error::subs::try(CODE(0x3eb6d58), HASH(0x3eb74b8)) called at /home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 4215</div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::_go(Process::MpiChunk=HASH(0x3e90218), "run", HASH(0x3e81748), 1, 4) called at /home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 341</div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::run(Process::MpiChunk=HASH(0x3e90218), 0) called at /home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 357</div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x3e90218), 0) called at /home/cvargas/maker/bin/../lib/Process/MpiTiers.pm line 287</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3ea34b8), 0) called at /home/cvargas/maker/bin/../lib/Process/MpiTiers.pm line 287</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3e733e8), 0) called at /home/cvargas/maker/bin/maker line 670</div><div>--> rank=NA, hostname=Ritchie</div><div>ERROR: Failed while annotating transcripts</div><div>ERROR: Chunk failed at level:1, tier_type:4</div><div>FAILED CONTIG:2973</div><div><br></div><div>ERROR: Chunk failed at level:6, tier_type:0</div><div>FAILED CONTIG:2973</div><div><br></div><div>examining contents of the fasta file and run log</div></div><div><br></div></div></div>
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