RNAmmer running

Question

[kishorssf91]

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"

**for linux

HMMSEARCHBINARY="/mnt/genome3/LabUsers/Kishor/DISK2/softwares/hmmer2/hmmer−2.3.2/src/"
  $PERL = "/usr/bin/perl"

I also changed the hmmsearch name to 'hmmsearch2 '. And in subsequent running i use the program like as:

./rnammer -S euk -m tsu,lsu,ssu -gff blood.gff -h hmm.out -f bloodRNA.fa /mnt/mnspt1/blood/rsem_outdir/blood.Trinity.RSEM.retained.clustered.fasta

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.

Answer 1

[Mensur Dlakic]

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:

/mnt/genome3/LabUsers/Kishor/DISK_2/softwares/hmmer2/hmmer−2.3.2/src/hmmsearch2   (or maybe DISK2)

[kishorssf91]

Hi @Mansur Thanks a lot for your kind and quick respose. The path i pasted above that took some error and i dont know why. The correct path is Disk_2. Anyway, you were correct that it requires directly the binary file of hmmsearch2 rather than the directory path only. Now it is working. Thanks again.