[maker-devel] Maker error message

[Daniel Ence]

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>


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</quote>
Quoted from:
http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html