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<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">
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<div style="direction: ltr;" id="divRpF633050"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Carson Holt [carsonhh@gmail.com]<br>
<b>Sent:</b> Tuesday, June 25, 2013 8:55 PM<br>
<b>To:</b> Jingjing Jin; maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] start position for some genes results<br>
</font><br>
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<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>
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<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>
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<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">
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<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>
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<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>
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<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>
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<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>
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