[maker-devel] MAKER error Failed while polishing proteins

[Carson Holt]

Glad it’s working.  MAKER does some things to fix issues with long seq IDs in BLAST etc. by assigning temporary IDs and then translating back to the original ID, but because the ones in your file were so long it triggered a different issue with maximum length of file names.

—Carson



> On Oct 27, 2014, at 10:49 AM, Sivaranjani Namasivayam <ranjani at uga.edu> wrote:
> 
> Hi Carson,
> 
> The fasta headers were the problem, when I shortened them the run completed sucessfully. Although for other scaffolds too there were similar such long fasta headers but it worked fine.
> 
> Thanks!
> Ranjani
> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: Monday, October 27, 2014 12:18 PM
> To: Sivaranjani Namasivayam
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] MAKER error Failed while polishing proteins
>  
> There is one warning message and one error message.
> 
> First this one —>
> WARNING: The fasta file contains sequences with names longer
> than 78 characters.  Long names get trimmed by BLAST, making
> it harder to identify the source of an alignmnet. You might
> want to reformat the fasta file with shorter IDs.
> File_name:/escratch3/ranjani/ranjani_Oct_16/sn1_comparisons/uniprot_top_hits_sn1prot.fa
> 
> Also this one —> sh: File name too long
> 
> The cause of your failures are the long sequence identifiers in your fasta. There are actually several potential downstream issues as a result, but the most immediate is that some temporary file names are going to be based off the sequence ID, and because your seq IDs are really long, they result in file names that are bigger than the largest allowed filename for the system.
> 
> Here is one example of a long ID I see in your STDERR —>
> SRCN_4312|tg_ortholog:TGME49_201150|EC:EC:3.6.3.12;EC:3.6.3.4;EC:3.6.3.8|scaff:scaffold00018|start:414787|end:435051|blastp_output:gi:401406237:ref:XP_003882568.1:
> 
> You need to reformat the header of each FASTA entry to make it shorter, not just for MAKER but for programs MAKER uses. Sequence Identifiers should be separated from other comment information in the FASTA header by spaces or else the comments become part of the identifier in accordance with FASTA format.
> 
> Thanks,
> Carson
> 
> 
>> On Oct 26, 2014, at 2:35 PM, Sivaranjani Namasivayam <ranjani at uga.edu <mailto:ranjani at uga.edu>> wrote:
>> 
>> Hi Carson,
>> 
>> Attaching the error file. (The file is too big to be posted to the mailing list). There are a number of errors reported about the fasta file, but I see these errors for the other scaffolds too and I get predictions and they run finished successfully , so I thought these errors might not be the reason..
>> 
>> Thanks,
>> Ranjani
>> 
>> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>> Sent: Thursday, October 23, 2014 3:20 PM
>> To: Sivaranjani Namasivayam
>> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] MAKER error Failed while polishing proteins
>>  
>> The causal error will be further up the error log. You may just want to send your capture STDERR file.
>> 
>> —Carson
>> 
>> 
>> 
>>> On Oct 23, 2014, at 1:05 PM, Sivaranjani Namasivayam <ranjani at uga.edu <mailto:ranjani at uga.edu>> wrote:
>>> 
>>> Hi,
>>> 
>>> I get this error when I run MAKER
>>> 
>>> ERROR: Failed while polishing proteins
>>> ERROR: Chunk failed at level:10, tier_type:3
>>> FAILED CONTIG:scaffold00006
>>> 
>>> ERROR: Chunk failed at level:4, tier_type:0
>>> FAILED CONTIG:scaffold00006
>>> 
>>> Other scaffolds run fine, but this scaffold keeps failing. Would it mean something is wrong with the proteins in this scaffold?
>>> 
>>> Thanks,
>>> Ranjani
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>> 
>> <submpi2.sh.e5771113.zip>
> 
> 

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