[maker-devel] ERROR: Failed while processing the chunk divide!!

Tue Feb 11 15:59:57 MST 2014

Hi Hossen, 

I think that what would be the most help right now is if you ran MAKER on only one of those contigs that are failing and send me the entire error output along with the maker control files that you are using. It looks like the error is coming from the gff3 files that you are using as input. 

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: Borhan, Hossein [Hossein.Borhan at AGR.GC.CA]
Sent: Tuesday, February 11, 2014 3:51 PM
To: Daniel Ence
Subject: ERROR: Failed while processing the chunk divide!!

Dear Daniel

I re-started maker and it is still running. But in error our file that has
been generated so far it seems that smaller conitgs are affected. There
are contigs of 2-4 kb with this error but also I noticed a contig of 30kb
length having this error

I was wondering if I need to change the setting in the maker_opt file

#-----MAKER Behavior Options
max_dna_len=100000 #length for dividing up contigs into chunks
(increases/decreases  memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often
useless)

If I understand correctly max_dna_len   divide conitgs  of over 100kb to
smaller chucks. However it is not clear to me that for the min_contig
option if the default contig length is 10kb or less, then why I have error
message for 30kb long contigs. Should I change this to 0

Here is an example of the error message for one of the contigs

#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/exonerate-2.2.0-x86_64/bin/exonerate  -q
/raid01/projects/Plasmodiophora/brassicae/PT3/version2/Maker-config/P.brass
icae.PT3.v1.genome.maker.output/P.brassicae.PT3.v1.genome_datastore/35
/17/PbPT3Sc00001//theVoid.PbPT3Sc00001/comp14545_c0_seq1.fasta
-t
/raid01/projects/Plasmodiophora/brassicae/PT3/version2/Maker-config/P.brass
icae.PT3.v1.genome.maker.output/P.brassicae.PT3.v1.genom
e_datastore/35/17/PbPT3Sc00001//theVoid.PbPT3Sc00001/PbPT3Sc00001.235-1136.
fasta
-Q dna -T dna --model est2genome
--minintron 20 --showcigar --percent 20 >
/raid01/projects/Plasmodiophora/brassica
e/PT3/version2/Maker-config/P.brassicae.PT3.v1.genome.maker.output/P.brassi
cae.PT3.v1.genome_datastore/35/17/PbPT3Sc00001//theVoid.PbPT3Sc00001/PbPT3S
c00001.235-1136.comp14545_c0_seq1.est_exonerate
#-------------------------------#
cleaning blastn...
cleaning tblastx...
cleaning blastx...
ERROR: Failed on
PbPT3Sc00001_S_0.8_1-mRNA-1
Check your input GFF3 file for errors!
(from GFFDB)

FATAL ERROR
ERROR: Failed while processing the chunk
divide!!

ERROR: Chunk failed at level 17
!!
FAILED CONTIG:PbPT3Sc00001

--Next Contig--

Regards

HB

On 14-02-11 12:37 PM, "Daniel Ence" <dence at genetics.utah.edu> wrote:

>Hossein,
>
>Ok. So since this error came up on a local install, I'm going to need
>some more information to understand what went wrong. Is it the same
>contig that always causes this error? If it is, then is the the only
>error or warning that MAKER encounters while running on this contig? Or,
>if multiple contigs fail, then is it always the same error?
>
>If you can narrow it down to the smallest possible dataset that
>consistently gives the same error, then we canb egin to understand what's
>wrong.
>
>Thanks,
>Daniel
>
>
>Daniel Ence
>Graduate Student
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>________________________________________
>From: Borhan, Hossein [Hossein.Borhan at AGR.GC.CA]
>Sent: Tuesday, February 11, 2014 11:20 AM
>To: Daniel Ence
>Subject: Re: [maker-devel] Falied to create new account
>
>Hi Daniel
>
>I running it through the local server at my work
>
>
>
>
>
>
>M. Hossein Borhan, Ph.D.
>Research Scientist/ Chercheur Scientifique
>Saskatoon Research Centre/Centre de Recherches de Saskatoon
>Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada
>107 Science Place, Saskatoon, SK.,S7N 0X2
>Telephone/Téléphone: (306) 385-9441
>Facsimile/Télécopieur: (306) 385-9482
>Hossein.borhan at agr.gc.ca
>
>
>
>
>
>
>
>
>On 14-02-11 12:16 PM, "Daniel Ence" <dence at genetics.utah.edu> wrote:
>
>>Hi Hossein,
>>
>>Did you encounter this error while you were running MAKER on your local
>>machine or through the MAKER web annotation service?
>>
>>Thanks,
>>Daniel
>>
>>
>>Daniel Ence
>>Graduate Student
>>Eccles Institute of Human Genetics
>>University of Utah
>>15 North 2030 East, Room 2100
>>Salt Lake City, UT 84112-5330
>>________________________________________
>>From: Carson Holt [carsonhh at gmail.com]
>>Sent: Tuesday, February 11, 2014 10:18 AM
>>To: Daniel Ence
>>Cc: Mark Yandell
>>Subject: FW: [maker-devel] Falied to create new account
>>
>>Hey Daniel could you download his dataset, and see if you can replicate
>>the error.  Also check if this was an MWAS job or a local maker run (his
>>dataset will already be there for MWAS, you just need the job ID).
>>
>>Thanks,
>>Carson
>>
>>On 2/11/14, 10:16 AM, "Borhan, Hossein" <Hossein.Borhan at AGR.GC.CA> wrote:
>>
>>>Hi Carson
>>>
>>>
>>>I encountered this error while running maker
>>>
>>>FATAL ERROR
>>>ERROR: Failed while processing the chunk divide!!
>>>
>>>ERROR: Chunk failed at level 17
>>>!!
>>>FAILED CONTIG:PbPT3Sc00006
>>>
>>>
>>>
>>>
>>>
>>>HB
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>
>>
>>
>