[maker-devel] maker output- transcripts.fasta and proteins.fasta files missing

[Carson Holt]

Note protein/transcript fasts are only created when there are gene models to
output to those files (so their absence means there were no gene models for
that contig). Most sequences without protein/transcript fasts in your sample
are very short and thus don’t contain anything.  What is left either have no
est2genome results or the est2genome alignments do not have sufficient open
reading frame to be turned into a gene model (false merging of regions by
trinity can cause this, so make sure you use the jaccard index option when
assembling reads with trinity to avoid this).

You are using only the est2genome=1 option.  This will result in a limited
set of genes that can be used for training SNAP/Augustus (so not getting
results on all contigs is expected).  You really won’t get much as far as
results until you have one of the ab initio predictors turned on.

Thanks,
Carson


From:  dhivya arasappan <darasappan at gmail.com>
Date:  Tuesday, March 11, 2014 at 8:52 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Daniel Ence <dence at genetics.utah.edu>
Subject:  Re: maker output- transcripts.fasta and proteins.fasta files
missing

Alright done. My username is daras

Thanks
Dhivya

On Mar 10, 2014, at 5:10 PM, Carson Holt wrote:

> Input and compressed file of output.
> 
> Thanks,
> Carson
> 
> From:  dhivya arasappan <darasappan at gmail.com>
> Date:  Monday, March 10, 2014 at 2:09 PM
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  Daniel Ence <dence at genetics.utah.edu>
> Subject:  Re: maker output- transcripts.fasta and proteins.fasta files missing
> 
> Hi Carson,
> 
> Do you mean the whole maker output?
> 
> Thanks
> dhivya
> 
> On Mar 10, 2014, at 4:55 PM, Carson Holt wrote:
> 
>> Could you upload everything here —>
>> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>> 
>> Than send us the link generated or your user ID.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  dhivya arasappan <darasappan at gmail.com>
>> Date:  Monday, March 10, 2014 at 1:50 PM
>> To:  Carson Holt <carsonhh at gmail.com>, Daniel Ence <dence at genetics.utah.edu>
>> Subject:  Fwd: maker output- transcripts.fasta and proteins.fasta files
>> missing
>> 
>> Hi Carson and Daniel,
>> 
>> I'm sending this across to you separately since maker list is blocking my
>> email due to attachment size.
>> 
>> As always, thanks for any guidance you can provide.
>> Dhivya
>> 
>> 
>> Begin forwarded message:
>> 
>>> From: dhivya arasappan <darasappan at gmail.com>
>>> Date: March 10, 2014 3:14:03 PM CDT
>>> To: maker-devel at yandell-lab.org
>>> Subject: maker output- transcripts.fasta and proteins.fasta files missing
>>> 
>>>  
>>> Hello,
>>> 
>>> I've been running maker with different assembly files, reference files etc
>>> and I check the output by:
>>> 
>>> 1. concatenating the gff files
>>> 2. concatenating the *transcripts.fasta files
>>> 3. concatenating the *proteins.fasta files
>>> 
>>> I'm noticing that when I ran maker twice with same parameters, the second
>>> time around, many of the output subdirectories  do not have a
>>> *transcripts.fasta or *proteins.fasta file in it.
>>> There are 251 subdirectories and only 97 of them have all 3 output files.
>>> Maker log looks ok to me, but I've attached it here as well.
>>> 
>>> What could be the reason for this?
>>> 
>>> Thanks
>>> dhivya
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
> 



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