<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>Ok. This is fixed (along with a few other things), and is available for download as MAKER 2.25.</div><span id="OLK_SRC_BODY_SECTION"><div><div 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><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> Evan <<a href="mailto:eernst@cshl.edu">eernst@cshl.edu</a>><br><span style="font-weight:bold">Date: </span> Mon, 26 Mar 2012 09:29:45 -0700 (PDT)<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@googlegroups.com">maker-devel@googlegroups.com</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Can't call method "start" on an undefined value<br></div><div><br></div>Hi,<br><br>I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with the following error:<br><span style="font-family: 'courier new', monospace; "></span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">Preparing evidence for hint based annotation</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">cleaning clusters....</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">total clusters:1 now processing 0</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">in cluster::shadow_cluster...</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">...finished clustering.</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">cleaning clusters....</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; "> ...processing 0 of 3</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; "> ...processing 1 of 3</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; "> ...processing 0 of 2</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">Can't call method "start" on an undefined valueERROR: Failed while preparing evidence clusters for annotations</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">ERROR: Chunk failed at level:0, tier_type:3</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">FAILED CONTIG:scaffold93.1</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">ERROR: Chunk failed at level:7, tier_type:0</span><br style="font-family: courier new,monospace;"><span style="font-family: 'courier new', monospace; ">FAILED CONTIG:scaffold93.1</span><br style="font-family: courier new,monospace;"><br>This occurs when running just a single maker instance. <br><br>Thanks,<br>Evan<br>_______________________________________________
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