[maker-devel] Maker error message
Kapeel Chougule
kapeelc at gmail.com
Mon Dec 3 09:55:20 MST 2012
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.specific.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>
>>
>>
>> _______________________________________________
>> 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
> *
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-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
*
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