[maker-devel] MAKER error Failed while polishing proteins

[Sivaranjani Namasivayam]

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>
Sent: Monday, October 27, 2014 12:18 PM
To: Sivaranjani Namasivayam
Cc: 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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