<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">You can manually specify a path in maker_exe.ctl<br class=""><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 29, 2019, at 3:03 PM, Linnie Linnie <<a href="mailto:peachandolives@gmail.com" class="">peachandolives@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Dear Maker team,<div class=""><br class=""></div><div class="">I am analyzing a number of genomes in a cluster. I had previously installed RepeatMasker and RepeatModeler independently without problem in order to obtain the repeat libraries that are required by maker. This installation runs perfectly. </div><div class="">However, when I install maker, it does not recognize that a successful installation of RepeatMasker is already available. How can tell maker where RepeatMasker is already located? </div><div class=""><br class=""></div><div class="">I have alternatively tried to install RepeatMasker from within maker and then try to run maker. But it gives me the following error:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Compilation failed in require at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">BEGIN failed--compilation aborted at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: RepeatMasker failed</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=loma</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Failed while doing repeat masking</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Chunk failed at level:0, tier_type:1</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FAILED CONTIG:NQYS01000001.1</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Chunk failed at level:2, tier_type:0</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FAILED CONTIG:NQYS01000001.1</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">examining contents of the fasta file and run log</span></div></div><div class=""><br class=""></div><div class="">As a last option, I think I could run RepeatMasker with the installation I already have and then pass its .gff file to maker. In this case, which parameters should I pass in the maker_opts.ctl file? </div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thank you so much for all your help (and Happy New Year to everyone!)</div><div class="">L. </div></div></div></div>
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