<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 point of the failure you are seeing is occurring in the initialization stage, before reaching any of the changes that would have been introduced by 2.28. Try running the test data that comes with MAKER, does it fail as well?</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">jjin01@mail.rockefeller.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 25 June, 2013 9:53 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;">Yes, this is the real name.<br><br>
There is also no ":" in the name.<br><br>
Because I have use the same file for maker.2.27 and have no problem.<br><br>
I am not sure what is wrong with the new version.<br><br>
Jingjing<br><br><br><div style="font-family: Times New Roman; color: #000000; font-size: 16px"><hr tabindex="-1"><div style="direction: ltr;" id="divRpF876498"><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 9:47 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>Could you check for this sequence in your input genome file for "<span class="Apple-style-span" style="font-family:Tahoma; font-size:13px">processed_tobacco_genome_sequences_c1</span>", make sure that it is in fact that exact name, and there are no ':'
characters in the name because they can confuse the bioperl fasta indexer.</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" target="_blank">jjin01@mail.rockefeller.edu</a>><br><span style="font-weight:bold">Date: </span>Tuesday, 25 June, 2013 9:30 PM<br><span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>, "<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>RE: [maker-devel] start position for some genes results<br></div><div><br></div><div dir="ltr"><div 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><br>
I am so sorry. The problem is still here.<br><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>
at /home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiChunk.pm line 239.<br>
Process::MpiChunk::_prepare('Process::MpiChunk=HASH(0x4e16178)', 'HASH(0x4e10810)', 0) called at /home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiTiers.pm line 73<br>
Process::MpiTiers::__ANON__() called at /home/jingjing/software/maker.2.28/maker/bin/../lib/Error.pm line 415<br>
eval {...} called at /home/jingjing/software/maker.2.28/maker/bin/../lib/Error.pm line 407<br>
Error::subs::try('CODE(0x4e19100)', 'HASH(0x4e1bd58)') called at /home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiTiers.pm line 79<br>
Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x4e16e68)') called at /home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiTiers.pm line 56<br>
Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x4e16ad8)', 0, 'Process::MpiChunk') called at /home/jingjing/software/maker.2.28/maker/bin/./maker line 650<br>
--> rank=NA, hostname=ChuaServer1<br>
ERROR: Failed in tier preparation<br>
WARNING: You must always set a rank before running MpiTiers<br>
FATAL: argument `seq_id` does not exist in MpiTier object<br><br><div style="font-family:Times New Roman; color:#000000; font-size:16px"><hr tabindex="-1"><div id="divRpF633050" style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Carson Holt [<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>]<br><b>Sent:</b> Tuesday, June 25, 2013 8:55 PM<br><b>To:</b> Jingjing Jin; <a href="mailto:maker-devel@yandell-lab.org" target="_blank">
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>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" target="_blank">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" target="_blank">carsonhh@gmail.com</a>>, "<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>RE: [maker-devel] start position for some genes results<br></div><div><br></div><div dir="ltr"><div 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 id="divRpF917155" style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Carson Holt [<a href="mailto:carsonhh@gmail.com" target="_blank">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" target="_blank">
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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