Problem during class demo with maker

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Problem during class demo with maker

jim.hu.biobio
We ran the maker demo files tonight in our genomics class.  The instructor was able to get the output, but when the students ran maker, all of them got hung at the repeatmasker step.  They were all running it on the same Mac OSX server. 

genomics00:makerdata jimhu$ maker
A data structure will be created for you at:
/Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log




--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/usr/local/bioinfosoft/RepeatMasker/RepeatMasker /Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/theVoid.contig-dpp-500-500/contig-dpp-500-500.0 -species all -dir /Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/theVoid.contig-dpp-500-500 -pa 1
#-------------------------------#
<hangs here>

cross_match is taking all the cpu cycles when it hangs.

Any thoughts?  We're thinking it's creating some kind of race condition where people are killing each others' tmp files.  But we're grasping at straws!

Jim

 p.s. sent this with the wrong email address to the moderation queue

=====================================

Jim Hu

Associate Professor

Dept. of Biochemistry and Biophysics

2128 TAMU

Texas A&M Univ.

College Station, TX 77843-2128

979-862-4054




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Re: Problem during class demo with maker

Carson Hinton Holt
Re: [maker-devel] Problem during class demo with maker Two things.  There should be no race condition as long as each job is run in a separate directory, so make sure everyone runs under a separate directory.

Second, try installing the latest version of RepeatMasker with rmBlast rather than cross_match.  Unfortunately cross_match is extremely slow (I can’t over emphasize this).  It takes forever, and the RepeatMasker developers finally decided to build their own version of BLAST to use inside of RepeatMasker for this very reason.

Also, if this is for a class, you might want to consider trying MWAS (MAKER Web Annotation Service) at http://www.yandell-lab.org/software/mwas.html .

You can log in as a guest and load example jobs (the “D. melanogaster : Dpp” example would be the equivalent to the example files included with MAKER). You can also automatically  view results in GBrowse, JBrowse, Apollo, and SOBA. (when using these viewers, make sure to select the tracks you want to see once the tools load).

Thanks,
Carson

On 9/20/10 8:04 PM, "jim.hu.biobio" <jim.hu.biobio@...> wrote:

We ran the maker demo files tonight in our genomics class.  The instructor was able to get the output, but when the students ran maker, all of them got hung at the repeatmasker step.  They were all running it on the same Mac OSX server.

genomics00:makerdata jimhu$ maker
A data structure will be created for you at:
/Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log




--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/usr/local/bioinfosoft/RepeatMasker/RepeatMasker /Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/theVoid.contig-dpp-500-500/contig-dpp-500-500.0 -species all -dir /Network/Servers/genomics00.bio.tamu.edu/Users/jimhu/zzgenomics/lab04/makerdata/dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/theVoid.contig-dpp-500-500 -pa 1
#-------------------------------#
<hangs here>

cross_match is taking all the cpu cycles when it hangs.

Any thoughts?  We're thinking it's creating some kind of race condition where people are killing each others' tmp files.  But we're grasping at straws!

Jim

 p.s. sent this with the wrong email address to the moderation queue
=====================================

Jim Hu

Associate Professor

Dept. of Biochemistry and Biophysics

2128 TAMU

Texas A&M Univ.

College Station, TX 77843-2128

979-862-4054




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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org