[maker-devel] Maker error message

Wed Nov 28 13:15:13 MST 2012

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
*
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