<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>The correct file to update in Bioperl is /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm not Bioperl.pm, but technically you only have to fix whichever .pm file loads last. So if it's working then don't worry about it because one of the files fixed by the first command are loading after /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Hung Chih-Ming <<a href="mailto:ymwur1@gmail.com">ymwur1@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, 15 November, 2012 2:02 AM<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> segmentation fault (core dumped) for maker running<br></div><div><br></div>Hi Dr. Holt,<br><br>I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12.<br>But when I ran maker, I got an error message show segmentation fault (see below):<br><br>STATUS: Parsing control files...<br>
STATUS: Processing and indexing input FASTA files...<br>
程式記憶體區段錯誤 (core dumped)<br><br>I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib<br><br>"sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)"<br><br>Now maker seems to work!<br> <br>However, I could not follow the next step based on your response in the google discussion group,<br>"You may also have to run the fix below on wherever Bioperl is installed as
<br>well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File)
<br>statement in the Bio::DB::Fasta module in one of the BEGIN statements."<br><br>I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed:<br>sed: 沒有輸入檔案 (it means no input files)<br>I want to ask if this step is necessary? If so, what is the directory where I should run the fix?<br><br>Thanks,<br><br>Chih-Ming<br><br><br>Chih-Ming Hung<br>Postdoctoral researcher'<br>Department of Life Science<br>National Taiwan Normal University<br>Taipei, Taiwan<br>Email: <a href="mailto:ymwur1@gmail.com">ymwur1@gmail.com</a><br><br><br><br></span></body></html>