<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>Delete the mpi_blastdb directory before starting, to make sure all indexes get rebuilt. Also make sure you are not setting TMP= to a network mounted location.</div><div><br></div><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> Jingjing Jin <<a href="mailto:jjin01@mail.rockefeller.edu">jjin01@mail.rockefeller.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 25 June, 2013 8:53 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<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] start position for some genes results<br></div><div><br></div><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div ocsi="0" fpstyle="1" style="word-wrap:break-word; color:rgb(0,0,0); font-size:14px; font-family:Calibri,sans-serif"><div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Carson,
<br><br>
When I use the new version of maker, I have another problem like this:<br><br>
jingjing@ChuaServer1:~/project/$ /home/jingjing/software/maker.2.28/maker/bin/./maker<br>
STATUS: Parsing control files...<br>
STATUS: Processing and indexing input FASTA files...<br>
STATUS: Setting up database for any GFF3 input...<br>
A data structure will be created for you at:<br>
/home/jingjing/project/tobacco/Nicotiana_tabacum/maker.2.28/1/tobacco_seq_1.maker.output/tobacco_seq_1_datastore<br><br>
To access files for individual sequences use the datastore index:<br>
/home/jingjing/project/tobacco/Nicotiana_tabacum/maker.2.28/1/tobacco_seq_1.maker.output/tobacco_seq_1_master_datastore_index.log<br><br>
STATUS: Now running MAKER...<br>
WARNING: Cannot find >processed_tobacco_genome_sequences_c1, trying to re-index the fasta.<br>
stop here: processed_tobacco_genome_sequences_c1<br>
ERROR: Fasta index error<br><br><br>
Do you know how to fix this problem about new version?<br><br>
Thanks!<br><br>
Jingjing<br><br><br><br><div style="font-family: Times New Roman; color: #000000; font-size: 16px"><hr tabindex="-1"><div style="direction: ltr;" id="divRpF917155"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Carson Holt [<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>]<br><b>Sent:</b> Tuesday, June 25, 2013 6:55 PM<br><b>To:</b> Jingjing Jin; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] start position for some genes results<br></font><br></div><div></div><div><div>What MAKER version are you using? This should be fixed in the current 2.28. It only happened under a very specific set of circumstances, but I remember fixing it. So let me know if you are using 2.28.</div><div><br></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>Jingjing Jin <<a href="mailto:jjin01@mail.rockefeller.edu" target="_blank">jjin01@mail.rockefeller.edu</a>><br><span style="font-weight:bold">Date: </span>Tuesday, 25 June, 2013 5:13 PM<br><span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<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] start position for some genes results<br></div><div><br></div><div dir="ltr"><style id="owaParaStyle" type="text/css">
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BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;}P {margin-top:0;margin-bottom:0;}</style><div><div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear all,<br><br>
I find some strange things about location for my final result.<br><br>
Like for some start position of final gene model:<br><br><table border="0" cellpadding="0" cellspacing="0" width="1293"><colgroup><col width="110"><col span="7" width="64"><col width="735"></colgroup><tbody><tr height="20"><td style="height:15.0pt; width:83pt" height="20" width="110">c124062</td><td style="width:48pt" width="64">maker</td><td style="width:48pt" width="64">gene</td><td style="width:48pt" align="right" width="64">-1</td><td style="width:48pt" align="right" width="64">507</td><td style="width:48pt" width="64">.</td><td style="width:48pt" width="64">-</td><td style="width:48pt" width="64">.</td><td style="width:551pt" width="735">ID=maker-c124062-snap-gene-0.2;Name=maker-c124062-snap-gene-0.2</td></tr></tbody></table><br><br>
It start position is -1.<br><br>
Does someone know why the start position is -1?<br><br>
Is there something wrong?<br><br>
Thanks!<br><br>
Jingjing<br><br><br></div></div></div>
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