Problem during class demo with maker

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Problem during class demo with maker

Jim Hu
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

 

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

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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