<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=""><div class="">If running under MPI, you can get messages from multiple processes (slightly out of order), in which case the more descript cause of the error may be further upstream in the STDERR log. If running without MPI, and the error you see is matched with the Widget::RepeatMasker command used, then you can simply copy it and run it outside of MAKER. If there are installation issues with your RepeatMasker copy then the cause will become more apparent.</div><div class=""><br class=""></div><div class="">i.e. Run the command by itself —> /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 11, 2017, at 12:43 PM, Zach Cohen <<a href="mailto:zachary.pcohen@gmail.com" class="">zachary.pcohen@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello All,<div class="">I'm receiving a RepeatMasker on some (not all) of my scaffolds. </div><div class=""><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">Widget::RepeatMasker:</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">cd /tmp/maker_7hGhhm; /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">#-------------------------------#</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">ERROR: RepeatMasker failed</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">--> rank=NA, hostname=82853d8df2a5</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">ERROR: Failed while doing repeat masking</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">ERROR: Chunk failed at level:0, tier_type:1</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1">FAILED CONTIG:scaffold2852_size18614</span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">ERROR: Chunk failed at level:2, tier_type:0</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">FAILED CONTIG:scaffold2852_size18614</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class="">examining contents of the fasta file and run log</i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><i class=""><br class=""></i></span></p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1">I'm not sure if there is an issue with the widget itself, as this doesn't come up for all the scaffolds and the example data seemed to run fine, or a problem with these particular scaffolds. Thanks for any assistance you can provide!</span></p><p class="inbox-inbox-p1">Best,</p><p class="inbox-inbox-p1"><span class="inbox-inbox-s1">Z</span></p></div></div>
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