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Old 01-28-2018, 11:29 AM   #1
bgu
Junior Member
 
Location: Europe

Join Date: Dec 2011
Posts: 5
Default RepeatScout and RepeatMasker

I'm looking for help with running RepeatMasker on RepeatScout output. The documentation just says

"RepeatMasker is run on the sequence of interest using this filtered RepeatScout library."

RepeatScout is the most recent version. The first three steps run fine with the example data provided with RepeatScout (human3M.fa). A fasta output file (test2.fa) is the result. RepeatMasker is the most recent version installed with hmmer 3.1b2 (precompiled).

The command line for RepeatMasker is:

perl ../RepeatMasker/RepeatMasker human3M.fa -lib test2.fa

The output is

RepeatMasker version open-4.0.7
Search Engine: HMMER [ 3.1b2 (February 2015) ]
RepeatMasker::createLib(): Error invoking /usr/local/bin/hmmpress on file /home/au154761/src/sci/RepeatScout-master/RM_20800.SunJan282116242018/test2.fa.

It seems that hmmer requires some format other than fasta, but RepeatScout does not provide any guidance.

Any suggestions?
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fasta format, repeatmasker, repeatscout

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