<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>This message —> "Can't locate MAKER/ConfigData.pm in @INC"</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">It tells me you did not finish installing MAKER. Make sure you follow the full instructions in the …/maker/INSTALL document. Also make sure you did not get any errors, and you ran the './Build install’ step.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div>MAKER/ConfigData.pm is created as part of the install and won’t exist unless it is successful. Other things that will also be created during the installation are …/maker/bin and …/maker/perl directories. If they are not there then the installation was not successful.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><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> Thursday, December 26, 2013 at 8:08 AM<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> Re: [maker-devel] Updated Maker, having issues...<br></div><div><br></div><div dir="ltr">Thanks so much for getting back to me! I did unpack the new version on top of our old version by mistake, unfortunately. I re-installed both 2.28 and 2.30 without doing that again and both are giving me the same error. I installed the BioPerl dependencies locally for Maker and it looks like it's not automatically pointing to those when running. How can I tell Maker to use the local dependencies? Do I need to bite the bullet and allow the Build script to overwrite the BioPerl dependencies for the whole server? There was a bit of an issue when I allowed Maker's Build to overwrite our version of Augustus...<div><br></div><div>Here's the maker error:</div><div><div>$ maker</div><div>Can't locate MAKER/ConfigData.pm in @INC (@INC contains: /home/usr/local/bin/../perl/lib /home/usr/local/bin/../lib /home/usr/local/bin/../src/inc/perl/lib /usr/local/lib/perl5/5.8.8 /usr/local/lib/perl5/x86_64-linux-thread-multi /usr/local/lib/perl5 /usr/local/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/local/lib64/perl5/5.8.8 /usr/local/lib64/perl5 /usr/local/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/local/lib64/perl5/site_perl/5.8.8 /usr/local/lib64/perl5/site_perl /usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl /usr/local/pkg/eval/lib/perl5 /usr/local/pkg/glean-gene/lib /usr/local/pkg/maker/lib /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/local/bin/maker line 45.</div><div>BEGIN failed--compilation aborted at /usr/local/bin/maker line 45.</div><div><br></div><div>When I look for the missing module:</div><div>$ locate ConfigData.pm</div><div>/home/usr/local/lib/perl5/Bio/ConfigData.pm</div><div>/home/usr/local/lib/perl5/site_perl/5.8.8/Module/Build/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.28/perl/lib/MAKER/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.28/perl/lib/Module/Build/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.28/src/blib/lib/MAKER/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.28/src/inc/bundle/Module/Build/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.30p-beta/perl/lib/MAKER/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.30p-beta/perl/lib/Module/Build/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.30p-beta/src/blib/lib/MAKER/ConfigData.pm</div><div>/home/usr/local/pkg/maker-2.30p-beta/src/inc/bundle/Module/Build/ConfigData.pm</div><div>/home/usr/local/src/bioperl/bioperl-run/blib/lib/Bio/ConfigData.pm</div><div>/home/usr/local/src/bioperl/branch-1-6/blib/lib/Bio/ConfigData.pm</div><div>/home/usr/local/src/bioperl/core/blib/lib/Bio/ConfigData.pm</div><div>/usr/lib/perl5/vendor_perl/5.8.8/Module/Build/ConfigData.pm</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Dec 20, 2013 at 4:00 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><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><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Emily Whiston <<a href="mailto:emwhist@gmail.com" target="_blank">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" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Updated Maker, having issues...<br></div><div><div class="h5"><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 style="white-space:pre-wrap"> </span>Process::MpiChunk::__ANON__() called at /usr/local/pkg/maker/lib/Error.pm line 415</div><div><span style="white-space:pre-wrap"> </span>eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 407</div><div><span style="white-space:pre-wrap"> </span>Error::subs::try(CODE(0x1f8c7430), HASH(0x1f955ed0)) called at /usr/local/pkg/maker/lib/Process/MpiChunk.pm line 4165</div><div><span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>Process::MpiTiers::__ANON__() called at /usr/local/pkg/maker/lib/Error.pm line 415</div><div><span style="white-space:pre-wrap"> </span>eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 407</div><div><span style="white-space:pre-wrap"> </span>Error::subs::try(CODE(0x1f895dd0), HASH(0x1f8c7130)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 375</div><div><span style="white-space:pre-wrap"> </span>Process::MpiTiers::_load_chunks(Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 185</div><div><span style="white-space:pre-wrap"> </span>Process::MpiTiers::next_chunk(Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 816</div><div><span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>Process::MpiTiers::__ANON__(Error::Simple=HASH(0x1f895970), SCALAR(0x1d6018c0)) called at /usr/local/pkg/maker/lib/Error.pm line 339</div><div><span style="white-space:pre-wrap"> </span>eval {...} called at /usr/local/pkg/maker/lib/Error.pm line 329</div><div><span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>Error::subs::try(CODE(0x1f8c7480), HASH(0x1f91cbd0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 79</div><div><span style="white-space:pre-wrap"> </span>Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x1f8b47c0)) called at /usr/local/pkg/maker/lib/Process/MpiTiers.pm line 56</div><div><span style="white-space:pre-wrap"> </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" target="_blank">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></div></div>
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