[maker-devel] start position for some genes results

[Carson Holt]

Could you check for this sequence in your input genome file for
"processed_tobacco_genome_sequences_c1", 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.

--Carson


From:  Jingjing Jin <jjin01 at mail.rockefeller.edu>
Date:  Tuesday, 25 June, 2013 9:30 PM
To:  Carson Holt <carsonhh at gmail.com>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  RE: [maker-devel] start position for some genes results

Dear Carson,


I am so sorry. The problem is still here.

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/jingjing/project/tobacco/Nicotiana_tabacum/maker.2.28/1/tobacco_seq_1.
maker.output/tobacco_seq_1_datastore

To access files for individual sequences use the datastore index:
/home/jingjing/project/tobacco/Nicotiana_tabacum/maker.2.28/1/tobacco_seq_1.
maker.output/tobacco_seq_1_master_datastore_index.log

STATUS: Now running MAKER...
WARNING: Cannot find >processed_tobacco_genome_sequences_c1, trying to
re-index the fasta.
stop here: processed_tobacco_genome_sequences_c1
ERROR: Fasta index error
 at /home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiChunk.pm
line 239.
        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
        Process::MpiTiers::__ANON__() called at
/home/jingjing/software/maker.2.28/maker/bin/../lib/Error.pm line 415
        eval {...} called at
/home/jingjing/software/maker.2.28/maker/bin/../lib/Error.pm line 407
        Error::subs::try('CODE(0x4e19100)', 'HASH(0x4e1bd58)') called at
/home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiTiers.pm line
79
        Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x4e16e68)')
called at 
/home/jingjing/software/maker.2.28/maker/bin/../lib/Process/MpiTiers.pm line
56
        Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x4e16ad8)', 0,
'Process::MpiChunk') called at
/home/jingjing/software/maker.2.28/maker/bin/./maker line 650
--> rank=NA, hostname=ChuaServer1
ERROR: Failed in tier preparation
WARNING: You must always set a rank before running MpiTiers
FATAL: argument `seq_id` does not exist in MpiTier object


From: Carson Holt [carsonhh at gmail.com]
Sent: Tuesday, June 25, 2013 8:55 PM
To: Jingjing Jin; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] start position for some genes results

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.

--Carson


From: Jingjing Jin <jjin01 at mail.rockefeller.edu>
Date: Tuesday, 25 June, 2013 8:53 PM
To: Carson Holt <carsonhh at gmail.com>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject: RE: [maker-devel] start position for some genes results

Dear Carson, 

When I use the new version of maker, I have another problem like this:

jingjing at ChuaServer1:~/project/$
/home/jingjing/software/maker.2.28/maker/bin/./maker
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/jingjing/project/tobacco/Nicotiana_tabacum/maker.2.28/1/tobacco_seq_1.
maker.output/tobacco_seq_1_datastore

To access files for individual sequences use the datastore index:
/home/jingjing/project/tobacco/Nicotiana_tabacum/maker.2.28/1/tobacco_seq_1.
maker.output/tobacco_seq_1_master_datastore_index.log

STATUS: Now running MAKER...
WARNING: Cannot find >processed_tobacco_genome_sequences_c1, trying to
re-index the fasta.
stop here: processed_tobacco_genome_sequences_c1
ERROR: Fasta index error


Do you know how to fix this problem about new version?

Thanks!

Jingjing




From: Carson Holt [carsonhh at gmail.com]
Sent: Tuesday, June 25, 2013 6:55 PM
To: Jingjing Jin; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] start position for some genes results

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.

--Carson



From: Jingjing Jin <jjin01 at mail.rockefeller.edu>
Date: Tuesday, 25 June, 2013 5:13 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] start position for some genes results

Dear all,

I find some strange things about location for my final result.

Like for some start position of final gene model:

c124062makergene-1507.-.ID=maker-c124062-snap-gene-0.2;Name=maker-c124062-sn
ap-gene-0.2

It start position is -1.

Does someone know why the start position is  -1?

Is there something wrong?

Thanks!

Jingjing


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