<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>I’d need the full error to tell you anything. You can redirect STDERR to a file and attach it to an e-mail. But a few gerneral things to check would be that your /tmp directory is not full, that you did not set TMP= in the maker_opt.ctl file to an NFS mounted location, and if you are using OpenMPI make sure you have set LD_PRELOAD to the appropriate value as required for use of OpenMPI’s shared libraries.</div><div><br></div><div>Example —></div><div>export LD_PRELOAD=/usr/local/openmpi/lib/libmpi.so</div><div><br></div><div>If LD_PRELOAD was the issue, you need to make sure it was set before even installing MAKER or it will not compile correctly (fresh reinstall required when this happens). </div><div><br></div><div>Also make sure that when you were updating MAKER, you did not not unpack the new version tarball ontop of the old version of MAKER. Binaries will not be updated through the unpack process, and will require you to reinstall from scratch.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Emily Whiston <<a href="mailto:emwhist@gmail.com">emwhist@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, December 17, 2013 at 7:35 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] Updated Maker, having issues...<br></div><div><br></div><div dir="ltr">Hi,<div>I updated our version of Maker today and I'm running into issues... I'm getting the following error message (it's LONG, so this is just the top bit):<br><br></div><div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::__ANON__() called at /usr/local/pkg/maker/lib/Error.pm line 415</div><div><span class="" style="white-space:pre"> </span>eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 407</div><div><span class="" style="white-space:pre"> </span>Error::subs::try(CODE(0x1f8c7430), HASH(0x1f955ed0)) called at /usr/local/pkg/maker/lib/Process/MpiChunk.pm line 4165</div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::_go(Process::MpiChunk=HASH(0x1f8b4b80), "load", HASH(0x1f8b4960), 0, 0) called at /usr/local/pkg/maker/lib/Process/MpiChunk.pm line 316</div><div><span class="" style="white-space:pre"> </span>Process::MpiChunk::_loader(Process::MpiChunk=HASH(0x1f8b4b80), HASH(0x1f8b4960), 0, 0, Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 364</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::__ANON__() called at /usr/local/pkg/maker/lib/Error.pm line 415</div><div><span class="" style="white-space:pre"> </span>eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 407</div><div><span class="" style="white-space:pre"> </span>Error::subs::try(CODE(0x1f895dd0), HASH(0x1f8c7130)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 375</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::_load_chunks(Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 185</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::next_chunk(Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 816</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::_handler(Process::MpiTiers=HASH(0x1f8b47c0), Error::Simple=HASH(0x1f895970), "Failed in tier preparation") called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 78</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::__ANON__(Error::Simple=HASH(0x1f895970), SCALAR(0x1d6018c0)) called at /usr/local/pkg/maker/lib/Error.pm line 339</div><div><span class="" style="white-space:pre"> </span>eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 329</div><div><span class="" style="white-space:pre"> </span>Error::subs::run_clauses(HASH(0x1f91cbd0), "Can't call method \"get_Seq_by_id\" on an undefined value at /u"..., undef, ARRAY(0x1d614c50)) called at /usr/local/pkg/maker/lib/Error.pm line 426</div><div><span class="" style="white-space:pre"> </span>Error::subs::try(CODE(0x1f8c7480), HASH(0x1f91cbd0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 79</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 56</div><div><span class="" style="white-space:pre"> </span>Process::MpiTiers::new("Process::MpiTiers", HASH(0x1cd3e520), 0, "Process::MpiChunk") called at /usr/local/bin/maker line 259</div><div><br></div><div>
FATAL ERROR</div><div>ERROR: Failed while examining contents of the fasta file and run log</div><div><br></div><div>FATAL ERROR</div><div><br></div><div>FATAL ERROR</div><div>ERROR: Can not load chunks</div><div>WARNING: You must always set a rank before running MpiTiers</div><div>FATAL: argument `out_dir` does not exist in MpiTier object</div></div><div><br></div><div><br></div><div>I found another thread in the mailing list with the same error message and tried the advice there, but to no avail... <a href="http://gmod.827538.n3.nabble.com/Can-map2assembly-be-run-outside-the-maker-pipeline-tt4032901.html#a4032997">http://gmod.827538.n3.nabble.com/Can-map2assembly-be-run-outside-the-maker-pipeline-tt4032901.html#a4032997</a><br><br><br>I am running Maker with Snap and Augustus, using RNAseq-derived EST evidence and gene models from a close relative. Any advice would be much appreciated, as I'm rather desperate to get this up and running...</div><div><br></div><div><br></div><div>Best,</div><div><br></div><div>Emily</div></div>
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