[maker-devel] start position for some genes results

[Carson Holt]

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


_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130625/579b370e/attachment-0003.html>