[maker-devel] MAKER error Failed while polishing proteins

[Sivaranjani Namasivayam]

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

[Carson Holt]

The causal error will be further up the error log. You may just want to send your capture STDERR file.

—Carson

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[Carson Holt]

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 <ran...@uga.edu> wrote:

---

From: Carson Holt <cars...@gmail.com>
Sent: Thursday, October 23, 2014 3:20 PM
To: Sivaranjani Namasivayam
Cc: maker...@yandell-lab.org
Subject: Re: [maker-devel] MAKER error Failed while polishing proteins

 

<submpi2.sh.e5771113.zip>

[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 <cars...@gmail.com>
Sent: Monday, October 27, 2014 12:18 PM

[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

[Sivaranjani Namasivayam]

---

From: Carson Holt <cars...@gmail.com>
Sent: Thursday, October 23, 2014 3:20 PM
To: Sivaranjani Namasivayam
Cc: maker...@yandell-lab.org
Subject: Re: [maker-devel] MAKER error Failed while polishing proteins

 

[Sivaranjani Namasivayam]

Attaching the error file. There are a number of errors reported about the fasta file, but I see these errors for the other scaffolds too, so I thought these errors might not be the reason..

Thanks,

Ranjani

---

From: Carson Holt <cars...@gmail.com>
Sent: Thursday, October 23, 2014 3:20 PM
To: Sivaranjani Namasivayam
Cc: maker...@yandell-lab.org
Subject: Re: [maker-devel] MAKER error Failed while polishing proteins