<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>Use this command to check out the latest unreleased test version, and lt me know if you still get the error.</div><div><br></div><div>Command --> svn co svn://malachite.genetics.utah.edu/maker/trunk maker</div><div><br></div><div>User: yandell_guest</div><div>Password: y@ndell_Gu3st</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></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> Scott Geib <<a href="mailto:smg283@gmail.com">smg283@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 22 May, 2012 2:42 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] can't call method strand on an undefined value ERROR: Failed while flattening protein clusters<br></div><div><br></div>Hi, <br>Using maker 2.24, I am getting the following error (see below) in protein2genome widget. I also get the same error with est2genome. This happens with my own data (testing on a single scaffold), but not with the test data supplied with maker (dpp files in data folder). <br>
Scott<br><br><br>Widget::exonerate::protein2genome:<br>/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -q /data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI000194D3FC.for.1588546-1589203.9.fasta -t /data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9<br>
#-------------------------------#<br>cleaning blastx...<br>in cluster::shadow_cluster...<br>...finished clustering.<br>cleaning clusters....<br>total clusters:2 now processing 0<br> ...processing 0 of 23<br> ...processing 1 of 23<br>
...processing 2 of 23<br> ...processing 3 of 23<br> ...processing 4 of 23<br> ...processing 5 of 23<br> ...processing 6 of 23<br> ...processing 7 of 23<br> ...processing 8 of 23<br> ...processing 9 of 23<br> ...processing 10 of 23<br>
...processing 11 of 23<br> ...processing 12 of 23<br> ...processing 13 of 23<br> ...processing 14 of 23<br> ...processing 15 of 23<br> ...processing 16 of 23<br> ...processing 17 of 23<br> ...processing 18 of 23<br> ...processing 19 of 23<br>
...processing 20 of 23<br> ...processing 21 of 23<br>total clusters:2 now processing 0<br>in cluster::shadow_cluster...<br>...finished clustering.<br>cleaning clusters....<br>total clusters:2 now processing 0<br> ...processing 0 of 20<br>
...processing 1 of 20<br> ...processing 2 of 20<br> ...processing 3 of 20<br> ...processing 4 of 20<br> ...processing 5 of 20<br> ...processing 6 of 20<br> ...processing 7 of 20<br> ...processing 8 of 20<br> ...processing 9 of 20<br>
...processing 10 of 20<br> ...processing 11 of 20<br> ...processing 12 of 20<br> ...processing 13 of 20<br> ...processing 14 of 20<br> ...processing 15 of 20<br> ...processing 16 of 20<br> ...processing 17 of 20<br> ...processing 18 of 20<br>
total clusters:2 now processing 0<br>Can't call method "strand" on an undefined valueERROR: Failed while flattening protein clusters<br>ERROR: Chunk failed at level:11, tier_type:2<br>FAILED CONTIG:scaffold00001<br><br>
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