Dear, I am Kishor from Shanghai. Recently I have been trying to use RNAmmer. But yet to successfully run it. I have made two changes in the rnammer according to instructions, like as follows:
my $INSTALL_PATH = “/mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/RNAmmer”
$PERL = “/usr/bin/perl”
I also changed the hmmsearch name to ‘hmmsearch2 ‘. And in subsequent running i use the program like as:
This cmd only generates two files named “temp.145363.fsa” and “145363.lsu.cf”. There is no gff or any output besides two. Later i run the program “core-rnammer” like as follows: ./core-rnammer 145363.lsu.cf
But still could not find anything new. It’s getting to be a trouble for me and also I didn’t not get any issue or tutorial regarding this from where I could get support. So it will be a great support for me if i get any suggestion or instruction to solve the issue. Thanks.
I see at least two problems here. First, in one instance above you have DISK_2/softwares and in the other DISK2/softwares. Setting aside the unlikely case that you have two separate disks called DISK_2 and DISK2, one of those two is likely to be wrong and needs to be fixed. I’ll make an educated guess that DISK_2 is correct since rnammer seems to work.
The HMMSEARCHBINARY variable needs to point to a file, not a directory. Based on the information your provided and my guess about the correct directory, it should be: