<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="">Do you mean sequence upstream of the gene? If that is the case you would probably have to write a script to do this.</div><div class=""><br class=""></div><div class="">BioPerl is one options that has several Perl modules that help with manipulating fasta sequences and many common biology tool file formats —> <a href="http://www.bioperl.org" class="">http://www.bioperl.org</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 26, 2015, at 12:10 PM, Won C Yim <<a href="mailto:wyim@unr.edu" class="">wyim@unr.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Dear Carson Holt,</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Thank you for your reply.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">I asked this issue to STAMPEDE and there’s no way to help me.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">I think we need to move another server for MAKER.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Thank you for your help.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">And I have a one more question.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Is there any way to extract upstream sequence from MAKER results?</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">I tried to extract upstream and downstream results from them, but it’s really hard to do it.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Regards,</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Won</div><br style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div id="bloop_sign_1422299321139853056" class="bloop_sign" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="font-family: helvetica, arial; font-size: 13px;" class="">-- <br class="">Yim, Won Cheol<br class=""><div style="font-family: Calibri, sans-serif; font-size: 14px;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 10.5pt; font-family: Calibri, sans-serif;" class="">MS330/Department of Biochemistry & Molecular Biology</span></div></div><div style="font-family: Calibri, sans-serif; font-size: 14px;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 10.5pt; font-family: Calibri, sans-serif;" class="">1664 N. Virginia Street</span></div></div><div style="font-family: Calibri, sans-serif; font-size: 14px;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 10.5pt; font-family: Calibri, sans-serif;" class="">University of Nevada, Reno</span></div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"></p><div style="font-family: Calibri, sans-serif; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 19px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""></div><div class=""><br class="webkit-block-placeholder"></div><div style="font-family: Calibri, sans-serif; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 19px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 10.5pt; font-family: Calibri, sans-serif;" class="">email:<span class="Apple-converted-space"> </span><a href="mailto:wyim@unr.edu" class="">wyim@unr.edu</a></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><br class=""></div></div></div></div></div><br style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><p style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">On January 23, 2015 at 11:17:41 AM, Carson Holt (<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>) wrote:</p><blockquote type="cite" class="clean_bq" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class=""></div><div class="">Stampede only has MVAPICH2. It does not have OpenMPI (even though it has been requested several times). OpenFabrics libraries (used by MVAPICH2) have a known issue that restricts programs from making system calls while running under MPI. A system call is when one program launches another (i.e. MAKER launching BLAST). For this reason MAKER does not work with MVAPICH2. It only works with OpenMPI.<div class=""><br class=""></div><div class="">You can still get it to work on MVAPICH2, but only on a single node. If you request more than one node then it will fail. The solution would be for TACC to install OpenMPI as an option on Stampede (like they have on Lonestar), but until that happens you can only run MAKER on a single node.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><div class=""><div class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Jan 22, 2015, at 10:51 PM, Won C Yim <<a href="mailto:wyim@unr.edu" class="">wyim@unr.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">Dear anyone whom may it concern,</div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">Hi!</div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">My name is Won Cheol Yim in University of Nevada, Reno.</div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">I try to run MAKER on TACC Stampede.</div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">It looks everything installed properly.</div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><div id="bloop_customfont" class="" style="margin: 0px;">==============================================================================</div><div id="bloop_customfont" class="" style="margin: 0px;">STATUS MAKER v2.31.8</div><div id="bloop_customfont" class="" style="margin: 0px;">==============================================================================</div><div id="bloop_customfont" class="" style="margin: 0px;">PERL Dependencies:VERIFIED</div><div id="bloop_customfont" class="" style="margin: 0px;">External Programs:VERIFIED</div><div id="bloop_customfont" class="" style="margin: 0px;">External C Libraries:VERIFIED</div><div id="bloop_customfont" class="" style="margin: 0px;">MPI SUPPORT:ENABLED</div><div id="bloop_customfont" class="" style="margin: 0px;">MWAS Web Interface:DISABLED</div><div id="bloop_customfont" class="" style="margin: 0px;">MAKER PACKAGE:CONFIGURATION OK</div><div id="bloop_customfont" class="" style="margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="margin: 0px;">And I installed Perl 5.18.4 with threads option.</div><div id="bloop_customfont" class="" style="margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="margin: 0px;">But I try to run it with MPI, it generated error.</div><div id="bloop_customfont" class="" style="margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="margin: 0px;">I assumed this problem came from ibrun in Stampede.</div><div id="bloop_customfont" class="" style="margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="margin: 0px;">Is there anyway to run it on Stampede?</div><div id="bloop_customfont" class="" style="margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="margin: 0px;">Here is my log.</div><div id="bloop_customfont" class="" style="margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="margin: 0px;"><div id="bloop_customfont" class="" style="margin: 0px;">TACC: Starting up job</div><div id="bloop_customfont" class="" style="margin: 0px;">TACC: Setting up parallel environment for MVAPICH ssh-based mpirun.</div><div id="bloop_customfont" class="" style="margin: 0px;">cat: /home1/02908/wyim/.sge/job..hostlist.kUm5vXw9: No such file or directory</div><div id="bloop_customfont" class="" style="margin: 0px;">sort: open failed: /home1/02908/wyim/.sge/job..hostlist.kUm5vXw9: No such file or directory</div><div id="bloop_customfont" class="" style="margin: 0px;">TACC: Setup complete. Running job script.</div><div id="bloop_customfont" class="" style="margin: 0px;">TACC: starting parallel tasks...</div><div id="bloop_customfont" class="" style="margin: 0px;">[c404-703.stampede.tacc.utexas.edu:mpirun_rsh][read_hostfile] Can't open hostfile `/home1/02908/wyim/.sge/job..hostlist.kUm5vXw9': (2)</div><div id="bloop_customfont" class="" style="margin: 0px;">TACC: MPI job exited with code: 1</div><div id="bloop_customfont" class="" style="margin: 0px;">TACC: Shutting down parallel environment.</div><div id="bloop_customfont" class="" style="margin: 0px;">TACC: Shutdown complete. Exiting.</div></div></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">Regards,</div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><br class=""></div><div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">Won</div><div id="bloop_sign_1421991416237999872" class="bloop_sign" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="" style="font-family: helvetica, arial; font-size: 13px;">-- <br class="">Yim, Won Cheol<br class="">Sent with Airmail</div></div></div></blockquote></div></div></div></div></div></div></div></span></blockquote></div></blockquote></div><br class=""></body></html>