[maker-devel] Maker error message

Carson Holt carsonhh at gmail.com
Mon Dec 3 12:28:40 MST 2012 

Good to know.  It must be covered by an existing bug fix.  I'm going to wrap
up the devel version as 2.27 in the next couple days and put it online.

Thanks,
Carson



From:  Kapeel Chougule <kapeelc at gmail.com>
Date:  Monday, 3 December, 2012 11:55 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Maker error message

Hi Carson,

The MAKER devel version worked like a charm on the failed chromosomes. But
the MAKER 2.2.6 ended up giving me the same ERROR when I re-run it.

Thank you,

Kapeel

On Thu, Nov 29, 2012 at 7:52 AM, Carson Holt <carsonhh at gmail.com> wrote:
> There should normally be more error message than that.  The module used to
> capture the error returns the string "Died" without an end line character when
> there is a problem capturing the STDERR of the failure (and I see that phrase
> here), so could you run this again and see if it produces a different message
> the second time.  Also I'm going to send you instructions on download the
> development version of MAKER in a separate message (off list).  It is easier
> for me to make changes and have you test them immediately that way.  Also
> there are already some bug fixes in the devel version so it's good to rule
> those out.
> 
> Thanks,
> Carson
> 
> 
> From:  Kapeel Chougule <kapeelc at gmail.com>
> Date:  Wednesday, 28 November, 2012 3:15 PM
> To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Maker error message
> 
> Attached is the maker_opts file. I am using my own customized repeat library
> and repeat_protein files. The length of the identifiers was shortened to < 50
> characters as in my previous run it complained for identifiers having > 50
> characters.  
> 
> Thank you,
> 
> Kapeel
> On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence <dence at genetics.utah.edu> wrote:
>> Hi Kapeel, 
>> 
>> Please keep this discussion on the maker-devel group, so we can get
>> everyone's input to help resolve this issue with maker.
>> 
>> Can you sen me the maker_opts file that you were using? The options that
>> might be relevant include the libraries you were giving repeatrunner and
>> repeatmasker.
>> 
>> 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: kapeelc at gmail.com [kapeelc at gmail.com]
>> Sent: Wednesday, November 28, 2012 11:39 AM
>> To: Daniel Ence
>> Subject: Re: Maker error message
>> 
>> Hi Daniel,
>> 
>> Here is the output around the error:
>> 
>> j_size:94   current j:76
>>  j_size:94   current j:77
>>  j_size:94   current j:78
>>  j_size:94   current j:79
>>  j_size:94   current j:80
>>  j_size:94   current j:81
>>  j_size:94   current j:82
>>  j_size:94   current j:83
>>  j_size:94   current j:84
>>  j_size:94   current j:85
>>  j_size:94   current j:86
>>  j_size:94   current j:87
>>  j_size:94   current j:88
>>  j_size:94   current j:89
>>  j_size:94   current j:90
>>  j_size:94   current j:91
>>  j_size:94   current j:92
>>  j_size:94   current j:93
>> ...finished clustering.
>> re reading repeat masker report.
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specif
>> ic.out
>> re reading blast report.
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header
>> %2Efasta.repeatrunner
>> deleted:1 hits
>> in cluster::shadow_cluster...
>> DiedERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:Chr5
>> 
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:Chr5
>> 
>> 
>> 
>> 
>> --Next Contig--
>> 
>> Processing run.log file...
>> 
>> Maker is now finished!!!
>> 
>> 
>> For RepeatMasker I am using wublast as the search engine.
>> 
>> The run log had this:
>> 
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64
>> LOGCHILD        
>> /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5
>> _datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64
>> DIED    RANK    0
>> DIED    COUNT   2
>> 
>> Is there way to skip the the failed chunk and move forward??
>> 
>> Thanks
>> 
>> Kapeel
>> 
>> <quote author='Daniel Ence'>
>> Hi Kapeel,
>> 
>> I think we need some more information about the settings that you're running
>> maker with. Can you give more of the output around the error? Also, since
>> maker is dying during the repeatmasking stage, can you tell us more about
>> the settings you have for RepeatMasker?
>> 
>> 
>> 
>> 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: maker-devel-bounces at yandell-lab.org
>> [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule
>> [kapeelc at gmail.com]
>> Sent: Tuesday, November 27, 2012 6:23 PM
>> To: maker-devel at yandell-lab.org
>> Subject: [maker-devel] Maker error message
>> 
>> Hi,
>> 
>> I recently ran into this error for chr5. I am using maker 2.26 .
>> 
>> DiedERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:Chr5
>> 
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:Chr5
>> 
>> Could someone help me understand this error and why its happening?
>> 
>> Thanks,
>> 
>> --
>> 
>> Kapeel Chougule
>> Systems Programmer
>> Arizona Genomics Institute (AGI)
>> Thomas W. Keating Bioresearch Building
>> University of Arizona
>> 1657 E. Helen Street
>> Tucson, AZ 85719
>> www.genome.arizona.edu <http://www.genome.arizona.edu>
>> <http://www.genome.arizona.edu>
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> </quote>
>> Quoted from:
>> http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html
> 
> 
> 
> -- 
> 
> Kapeel Chougule
> Systems Programmer
> Arizona Genomics Institute (AGI)
> Thomas W. Keating Bioresearch Building
> University of Arizona
> 1657 E. Helen Street
> Tucson, AZ 85719 
> www.genome.arizona.edu <http://www.genome.arizona.edu>
> 
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org



-- 

Kapeel Chougule
Systems Programmer
Arizona Genomics Institute (AGI)
Thomas W. Keating Bioresearch Building
University of Arizona
1657 E. Helen Street
Tucson, AZ 85719   
www.genome.arizona.edu <http://www.genome.arizona.edu>



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