Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RepeatMasker & RepeatScout Zimbobo Bioinformatics 40 04-29-2019 01:20 PM
RepeatScout and RepeatModeler error zhanghao Bioinformatics 2 02-02-2017 11:29 PM
RepeatScout make error yzzhang Bioinformatics 33 08-23-2016 12:22 AM
problem with RepeatScout heiya Bioinformatics 3 10-02-2012 10:44 AM
RepeatScout anna_sh Bioinformatics 2 05-06-2011 07:38 AM

Thread Tools
Old 01-28-2018, 11:29 AM   #1
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?
bgu is offline   Reply With Quote

fasta format, repeatmasker, repeatscout

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:51 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO