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

Thu Mar 13 10:47:25 MDT 2014

Thanks Carson for the response.  I understand that est2genome=1 does  
not use any ab initio gene predictions, but simply identifies ests  
based on alignment.  I'm a little confused because I ran maker on my  
assembly before, using the same parameters ( including est2genome=1).   
I got a very good result with > 20,000 transcripts and proteins.

Then I  was able to get an improved assembly, where many scaffolds  
were combined into superscaffolds. So I reran maker on this  
assembly.   Same parameters, same transcriptome and proteins files.   
Now, I see such drastically different results:  Only 500+ genes and  
transcripts.  My scaffolds are now bigger than before, so I'm not sure  
how this is happening.   These were the results I sent you.

Another odd thing I noticed (and I am hesitant to report this because  
perhaps it is due to some sort of error on my part):  I ran maker on  
the improved assembly the first time and maker did not complete in the  
48 hours I allocated.  But I had  19,000+ transcripts in the  
unfinished output.  When I reran maker, just changing the time  
allocated, it completed much faster, but is giving much fewer  
transcripts and proteins as output.  Could something like this happen?  
If not, then I'm guessing I must have changed something although I'm  
pretty sure that I did not change anything other than the time  
allocated. I've attached the trascripts and proteins files from the  
first time I ran maker on my improved assembly.

Thanks again for your help
Dhivya

On Mar 13, 2014, at 11:14 AM, Carson Holt wrote:

> 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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