<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hey Daniel,<div><br></div><div>We need to start running RepeatMasker with cross_match now that wublast is no longer available and ABBlast hasn't been released yet. Since we've always used wublast, I don't have an immediate answer to your question, but if cross_match is giving Seg Fault then you may need to send your error output to Phil Green (phg
[ a t ] u.washington.edu). You might also ask around your group and see if anyone has wublast installed so that you could use that for comparison.</div><div><br></div><div>B</div><strong> </strong><div><br></div><div><div><div>On Sep 28, 2009, at 7:58 AM, Daniel Standage wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Barry's and Carson's suggestions were helpful, and SNAP is no longer having any problems. However, solving the SNAP problem made some other problems evident. When I ran maker using the sample data, there were some errors generated by RepeatMasker (see maker_errors.log). So I tried running RepeatMasker with some sample data and got similar errors (see repeat_masker_*.log). I then looked into all of RepeatMasker's prerequisites, and everything seems to be working fine except for cross_match. It ran for about 5 seconds generating the output in cross_match_*.log, and then would have a seg fault. I'm not really sure what the problem is or how to address it. Any suggestions?<br> <br>Thanks,<br><br>Daniel Standage<br>Plant Genetics Lab<br>Brigham Young University<br><br><div class="gmail_quote">On Tue, Sep 22, 2009 at 9:21 PM, Carson Holt <span dir="ltr"><<a href="mailto:carson.holt@genetics.utah.edu" target="_blank">carson.holt@genetics.utah.edu</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Snap requires you to specify the location of the installation directory, and will not automatically locate the HMM directory by itself. To do this you must set the environmental variable ZOE to be the path to the snap installation directory.<div> <br></div><div>i.e. in you .bash_profile add something like the following.</div><div><br></div><div>export ZOE=/usr/local/snap</div><div><br></div><div>Please note that this is the location of the snap base directory and not the Zoe or HMM directories under snap.</div> <div><br></div><div>You will then need to restart your terminal or type 'source ~/.bash_profile' to finish loading all changes to your .bash_profile.</div><div><br></div><div>When ZOE is not set, you must supply the full path to the HMM rather than just the name, i.e. snaphmm:/usr/local/snap/HMM/fly</div> <div><br></div><div>Let me know if that fixes it for you.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br><div><div><div>On Sep 22, 2009, at 5:21 PM, Daniel Standage wrote:</div><br></div><blockquote type="cite"> <div><div></div><div>Hi all,<br><br>I am trying to get Maker working on our system. I finally have all of the prerequisites installed, and they all appear to be working fine. I'm now using the example data to test maker and it is not working. I created a directory for the test, copied over the test data, generated the control files, and made the following changes to the control files.<br> <ul><li>In maker_bopts.ctl</li><ul><li>blast_type:ncbi</li></ul><li>In maker_opts.ctl</li><ul><li>genome:dpp_contig.fasta</li><li>est:dpp_transcripts.fasta</li><li>protein:dpp_proteins.fasta<br></li><li>snaphmm:fly<br></li> <li>predictor:snap</li></ul></ul>Then when I run maker (using the command <font style="color: rgb(102, 102, 102);" size="2"><span style="font-family: courier new,monospace;">maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl</span></font>), it gives the following error message.<br> <br><font style="color: rgb(102, 102, 102);" size="2"><span style="font-family: courier new,monospace;">#----------------------</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">FATAL: failed!!</span><br style="font-family: courier new,monospace;"> <span style="font-family: courier new,monospace;">#----------------------</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">ERROR: The snaphmm specified for Snap/Fathom in maker_opts.ctl does not exist.</span></font><br> <br>I verified that there is a "fly" file in SNAP's HMM directory, so I don't know what could be causing this. Does anyone have any insight?<br><br>Thanks,<br><br>Daniel Standage<br>Plant Genetics Lab<br> Brigham Young University<br></div></div> _______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><br> </blockquote></div><br></div></div></blockquote></div><br> <span><cross_match_errors.log></span><span><cross_match_output.log></span><span><maker_errors.log></span><span><repeat_masker_errors.log></span><span><repeat_masker_output.log></span><span><ATT00001.txt></span></blockquote></div><br></div></body></html>