<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>I can't reproduce your issue, so it is probably something about your system or environment.</div><div><br></div><ol><li>Is you /tmp directory full (or whatever you have $TMPDIR environmental variable is set to). Use 'df -h /tmp' to check.</li><li>Are you running in a directory on an NFS drive? Is it true NFS or is it something like FUSE.</li><li>Is your current working directory full.</li><li>Are you setting TMP= in the control files to either an NFS mounted location or an in memory mounted location. Same issue if you are setting the system's TMPDIR environmental variable to one of these.</li><li>Is your default /tmp directory in fact locally mounted (some clusters set this to in memory scratch).</li><li>Even though you already checked, humor me and run this exact command --> /Volumes/Qnap/external/Linux_x86_64/ncbi-blast/bin/blastx -version</li></ol><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Dave Messina <<a href="mailto:online@davemessina.com">online@davemessina.com</a>><br><span style="font-weight:bold">Date: </span> Monday, May 5, 2014 at 12:05 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] MAKER / RepeatRunner configuration issue<br></div><div><br></div><div dir="ltr">Thanks for your quick reply, Carson.<div><br></div><div>I'm using BLAST+ version 2.2.28, and even after upgrading from MAKER 2.31 to 2.31.3, unfortunately I'm still seeing the same issue.</div><div><br></div><div>I've uploaded a new tarball containing the latest (failed) output on the dpp sample data.</div><div><br></div><div>Any thoughts you have on how to resolve this would be great.</div><div><br></div><div><br></div><div><div>Thanks!</div><div>Dave</div></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 5, 2014 at 11:53 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">Use BLAST+ version 2.2.28. Also Make sure you are not using an old version of MAKER (2.31.3 is current).</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br></div><div><font face="Calibri,sans-serif"><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/</a></font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif">--Carson</font></div><div><font face="Calibri,sans-serif"><br></font></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br></div><span style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt"><span style="font-weight:bold">From: </span> Dave Messina <<a href="mailto:online@davemessina.com" target="_blank">online@davemessina.com</a>><br><span style="font-weight:bold">Date: </span> Monday, May 5, 2014 at 10:48 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] MAKER / RepeatRunner configuration issue<br></div><div><div class="h5"><div><br></div><div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div>Hi,</div><div><br></div><div>Even with the sample data, I'm getting a "Sequence contains no data" error from blastx during the RepeatRunner phase.<br></div><div><br></div><div>I've uploaded a tarball with my run on the dpp sample data to the MAKER File Upload site (filename maker_test.tgz).</div><div><br></div><div>Could you please take a look and give me your thoughts?</div><div><br></div><div><br></div><div><div>Thanks!</div><span><font color="#888888"><div>Dave</div></font></span></div><div><br></div></div></div><br></div></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span></div></blockquote></div><br></div></span></body></html>