<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">You need to look at your STDERR as the datastorem log just gives you a summary of what failed but not why. The cause of the error will be somewhere in your job's STDERR. You can capture the STDERR to a file by redirecting it.<div class=""><br class=""></div><div class="">For example, in bash shell —> maker 2> stderr.log</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 2, 2015, at 7:57 AM, Pedro Barbosa <<a href="mailto:psbpedrobarbosa@gmail.com" class="">psbpedrobarbosa@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span style="font-size:12.8px" class="">Hello,</span><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">I'm unable to run MAKER properly as the datastore_index.log file shows a FAILED run for all the scaffolds.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">Inspecting the log files from the output directory i see that it always dies when repeatrunner is invoked.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><div class=""><i class="">STARTED scaff-1k.maker.output/scaff-1k_datastore/3A/5C/scaffold_13//theVoid.scaffold_13/0/scaffold_13.0.consensi%2Efa%2Eclassified%2Empi%2E10%2E9.specific.out</i></div><div class=""><i class="">FINISHED scaff-1k.maker.output/scaff-1k_datastore/3A/5C/scaffold_13//theVoid.scaffold_13/0/scaffold_13.0.consensi%2Efa%2Eclassified%2Empi%2E10%2E9.specific.out</i></div><div class=""><i class="">STARTED scaff-1k.maker.output/scaff-1k_datastore/3A/5C/scaffold_13//theVoid.scaffold_13/0/scaffold_13.0.te_proteins%2Efasta.repeatrunner</i></div><div class=""><i class="">DIED RANK 0:2:0:0</i></div><div class=""><i class="">DIED COUNT 1</i></div></div><div style="font-size:12.8px" class=""><i class=""><br class=""></i></div><div style="font-size:12.8px" class="">Afterwards, I realized that repeatrunner is no longer included internally in MAKER, so I installed and included it in the system path. The error remained.</div><div style="font-size:12.8px" class="">I tried to remove the parameter 'repeat_protein' from the opts control file, because apparently repeatrunner is called when we provide a set of transposable elements. No success again.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">I tested both with the MAKER v2.31.8 and v3.00.0 beta, but the problem doesn't seem to be version related. Please find attached the maker_opts file that i used to run.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">Could you help me with this ? </div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">Best regards,</div><div style="font-size:12.8px" class="">Pedro Barbosa</div></div>
<span id="cid:C5640A5F-B907-4385-BABF-D725156FB305@genetics.utah.edu"><maker_opts.ctl></span>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></body></html>