<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="">The issue is unrelated to MAKER. Likely something happened during your initial configuration that resulted in a partial file. Perhaps when you unpackaged RepBase. Whether you ran it inside or outside of MAEKR was not the issue.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 8, 2016, at 1:22 PM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com" class="">chenwenbo1020@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Carson,<div class=""><br class=""></div><div class="">Thank you! I re-install the RepeatMasker, and run it with "-species all" outside of MAKER. It was successfully finished. Then I run Maker, and there is no error. I am curious why RepeatMasker could not build these library files when it was run in the MAKER.</div><div class=""><br class=""></div><div class="">Thanks!</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Wenbo</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2016-03-07 16:54 GMT-05:00 Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">RepeatMasker doesn’t actually finish installing until after you run it at least once with the RepBase Libraries (i.e. first job with RepBase). During it’s very first run it builds a bunch of needed library files under …/RepeatMasker/Libraries/ or sometimes under ~/.RepeatMaskerCache/. The failure message you get is that it can’t build those files (which is a RepeatMasker error not a MAKER error). So RepeatMasker is either installed or configured incorrectly.<span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class="h5"><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Mar 7, 2016, at 2:01 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>> wrote:</div><br class=""><div class=""><div style="word-wrap:break-word" class="">Make sure you use the same library you are giving it with MAKER. You can also look at MAKER’s STDERR to see exactly what command MAKER was using to run RepeatMasker.<div class=""><br class=""></div><div class="">This error —> "RepeatMasker::createLib(): Error invoking /home/chenwb/programs/ncbi-blast-2.2.28+/bin/makeblastdb on file"</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">It’s not from MAKER. RepeatMasker is printing that error and then failing.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Mar 7, 2016, at 1:26 PM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com" target="_blank" class="">chenwenbo1020@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hi Carson,<div class=""><br class=""></div><div class="">Thank you for your reply. I installed RepeatMasker following the Installation in their website, and got these information below.</div><div class=""><br class=""></div><div class="">=============================</div><div class=""><div class="">Congratulations! RepeatMasker is now ready to use.</div><div class="">The program is installed with a full version of the repeat library:</div><div class=""> DFAM Library Version = Dfam_2.0</div><div class=""> RMLibrary Version = 20150807</div><div class=""> Repbase Version = 20150807</div></div><div class="">=============================</div><div class=""><br class=""></div><div class="">I run RepeatMasker directly on one scaffold, and got no error. So I am still confused by the error given by MAKER.</div><div class=""><br class=""></div><div class="">Thank you!</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Wenbo</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2016-03-06 15:13 GMT-05:00 Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Wenbo,<br class="">
<br class="">
The error is from RepeatMasker and not MAKER. It means that RepeatMasker is not installed and configured correctly. You will have to fix whatever is wrong with your installation, and then make sure you can get RepeatMasker to run correctly by itself before running it inside of MAKER (i.e. run RepeatMasker directly on some test data).<br class="">
<br class="">
Thanks,<br class="">
Carson<br class="">
<div class=""><div class=""><br class="">
<br class="">
> On Mar 5, 2016, at 7:10 PM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com" target="_blank" class="">chenwenbo1020@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi All,<br class="">
><br class="">
> I have run Maker (v2.31.8) successfully. Now I update RepeatMasker to v4.0.6. then I came with this error:<br class="">
><br class="">
> RepeatMasker::createLib(): Error invoking /home/chenwb/programs/ncbi-blast-2.2.28+/bin/makeblastdb on file /home/chenwb/programs/RepeatMasker/Libraries/20150807/general/simple.lib.<br class="">
> ERROR: RepeatMasker failed<br class="">
> --> rank=4, hostname=hostname<br class="">
> ERROR: Failed while doing repeat masking<br class="">
> ERROR: Chunk failed at level:0, tier_type:1<br class="">
> FAILED CONTIG:scaffold149<br class="">
><br class="">
><br class="">
> The RepeatMasker was corrected installed. Should I update Maker to V3.0?<br class="">
><br class="">
> Thank you!<br class="">
><br class="">
> Best regards,<br class="">
> Wenbo<br class="">
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