rnammer running error

[jjjscuedu]

Does anyone use the RNAmmer software to scan genome to find rRNA?

I have already edited the path of rnammer file including the path to hmmsearch.

However, when I run it like this on sample data:

perl rnammer -S bac -m lsu,ssu,tsu -gff test.gff -xml test.xml -h test_respot.txt example/ecoli.fsa


I got no result in the test.gff file.

Can anyone give me some suggestions? I have tried to ask in the official email address, but no one reply me?

Thanks!

Jingjing

[jjk]

I am not sure if you still have the problem but for people that will have the problem in the future...

When combining rnammer and hmmsearch keep in mind at least for me that hmmsearch 3.0 was not working. Use hmmsearch 2.2g, http://hmmer.janelia.org/software/archive

[cliffbeall]

Thanks, jjk

You really helped me out.

By the way, I got RNAmmer working on OSX Snow Leopard with the following steps:

1. Download and untar rnammer
2. Install perl add-ons - I use MacPorts:

$ sudo port install p5-getopt-long
$ sudo port install p5-xml-sax

2. Download and untar hmmer2.2
3. Replace config.guess and config.sub files in hmmer2.2 with ones from /usr/share/libtool/config/
4. Compile hmmer as described in hmmer INSTALL file
5. Edit the rnammer file to change $INSTALL_PATH and to replace the die "unknown_platform\n" with the locations of hmmer2.2 hmmsearch and perl (for MacPorts it's usually /opt/local/bin/perl)