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. <div>
<br></div><div>Thank you,</div><div><br></div><div>Kapeel<br><br><div class="gmail_quote">On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Kapeel, <br>
<br>
Please keep this discussion on the maker-devel group, so we can get everyone's input to help resolve this issue with maker. <br>
<br>
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.<br>
<br>
Thanks,<br>
Daniel <br>
<br>
<br>
Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>
________________________________________<br>
From: <a href="mailto:kapeelc@gmail.com">kapeelc@gmail.com</a> [<a href="mailto:kapeelc@gmail.com">kapeelc@gmail.com</a>]<br>
Sent: Wednesday, November 28, 2012 11:39 AM<br>
To: Daniel Ence<br>
Subject: Re: Maker error message<br>
<br>
Hi Daniel,<br>
<br>
Here is the output around the error:<br>
<br>
j_size:94 current j:76<br>
j_size:94 current j:77<br>
j_size:94 current j:78<br>
j_size:94 current j:79<br>
j_size:94 current j:80<br>
j_size:94 current j:81<br>
j_size:94 current j:82<br>
j_size:94 current j:83<br>
j_size:94 current j:84<br>
j_size:94 current j:85<br>
j_size:94 current j:86<br>
j_size:94 current j:87<br>
j_size:94 current j:88<br>
j_size:94 current j:89<br>
j_size:94 current j:90<br>
j_size:94 current j:91<br>
j_size:94 current j:92<br>
j_size:94 current j:93<br>
...finished clustering.<br>
re reading repeat masker report.<br>
/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<br>
re reading blast report.<br>
/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<br>
deleted:1 hits<br>
in cluster::shadow_cluster...<br>
<div class="im">DiedERROR: Failed while processing all repeats<br>
ERROR: Chunk failed at level:3, tier_type:1<br>
FAILED CONTIG:Chr5<br>
<br>
ERROR: Chunk failed at level:2, tier_type:0<br>
FAILED CONTIG:Chr5<br>
<br>
<br>
<br>
<br>
</div>--Next Contig--<br>
<br>
Processing run.log file...<br>
<br>
Maker is now finished!!!<br>
<br>
<br>
For RepeatMasker I am using wublast as the search engine.<br>
<br>
The run log had this:<br>
<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64<br>
LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64<br>
DIED RANK 0<br>
DIED COUNT 2<br>
<br>
Is there way to skip the the failed chunk and move forward??<br>
<br>
Thanks<br>
<br>
Kapeel<br>
<br>
<quote author='Daniel Ence'><br>
Hi Kapeel,<br>
<br>
I think we need some more information about the settings that you're running<br>
maker with. Can you give more of the output around the error? Also, since<br>
maker is dying during the repeatmasking stage, can you tell us more about<br>
the settings you have for RepeatMasker?<br>
<br>
<br>
<br>
Thanks,<br>
Daniel<br>
<br>
Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>
________________________________<br>
From: <a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a><br>
[<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] on behalf of Kapeel Chougule<br>
[<a href="mailto:kapeelc@gmail.com">kapeelc@gmail.com</a>]<br>
Sent: Tuesday, November 27, 2012 6:23 PM<br>
To: <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br>
Subject: [maker-devel] Maker error message<br>
<div><div class="h5"><br>
Hi,<br>
<br>
I recently ran into this error for chr5. I am using maker 2.26 .<br>
<br>
DiedERROR: Failed while processing all repeats<br>
ERROR: Chunk failed at level:3, tier_type:1<br>
FAILED CONTIG:Chr5<br>
<br>
ERROR: Chunk failed at level:2, tier_type:0<br>
FAILED CONTIG:Chr5<br>
<br>
Could someone help me understand this error and why its happening?<br>
<br>
Thanks,<br>
<br>
--<br>
<br>
Kapeel Chougule<br>
Systems Programmer<br>
Arizona Genomics Institute (AGI)<br>
Thomas W. Keating Bioresearch Building<br>
University of Arizona<br>
1657 E. Helen Street<br>
Tucson, AZ 85719<br>
</div></div><a href="http://www.genome.arizona.edu" target="_blank">www.genome.arizona.edu</a><<a href="http://www.genome.arizona.edu" target="_blank">http://www.genome.arizona.edu</a>><br>
<br>
<br>
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<br>
</quote><br>
Quoted from:<br>
<a href="http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html" target="_blank">http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html</a><br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><font face="'courier new', monospace"><b><div><br></div><div>Kapeel Chougule</div><div>Systems Programmer</div><div>Arizona Genomics Institute (AGI)</div>
<div>Thomas W. Keating Bioresearch Building</div><div>University of Arizona</div><div>1657 E. Helen Street</div><div>Tucson, AZ 85719 </div><div><a href="http://www.genome.arizona.edu" target="_blank">www.genome.arizona.edu</a></div>
</b></font><br>
</div>