Installing and running RNAmmer on Mac ("Unknown platform")

Question

[suzuBell]

I recently tried to user rnammer.

1. I first used the web browser version and uploaded a .fasta file. Unfortunately, this resulted in an error as my .fasta file contains more than 1,000,000 total residues (twice as much in fact).

2. I decided to try the command line version to see if it could accept input files larger than 1,000,000 total residues? I am using macOS High Sierra. I downloaded the rnammer-1.2 and hmmer-3.2.1. Then, I followed directions here and here regarding updating the file locations. I then tried to run the following command:

   rnammer -S 'bac' -m 'tsu' -gff output_gff -h output_hmmreport -f output_fasta sample1.fasta

which resulted in the error: "unknown platform"

This message seems to come from a section of the /user/local/bin/rnammer file:

# path to hmmsearch of HMMER package
chomp ( my $uname = `uname`);
my $HMMSEARCH_BINARY;
my $PERL;
if ( $uname eq "Linux" ) {
        $HMMSEARCH_BINARY = "/usr/local/bin/hmmsearch";
        $PERL = "/usr/bin/perl";
} elsif ( $uname eq "IRIX64" ) {
        $HMMSEARCH_BINARY = "/usr/local/bin/hmmsearch";
        $PERL = "/usr/sbin/perl";
} else {
        die "unknown platform\n";
}

I updated this file twice. Once such that the second line of the above file said:

chomp ( my $uname = `Linux`);

And again such that the second line of the above file said

chomp ( my $uname = `IRIX64`);

But I receive the same brief error. I would greatly appreciate any advice anyone on this forum may have to resolve this issue. Many thanks.

Answer 1

[Jianyu]

I'm not very familiar with perl, but it seems you should use

chomp (my $uname = "Linux")

instead of

chomp (my $uname = `Linux`)

` is used to call uname in shell

By the way, why do you want to run RNAmmer on mac? I think the code is very clear that it doesn't want to be run under Mac OS environment

[suzuBell]

Hi @yztxwd. Thanks for the comment. I tried changing the second line to both homp (my $uname = "Linux") and homp (my $uname = "IRIX64"). When I used "Linux", and ran the code rnammer -S bac -m tsu,ssu,lsu -gff output_gff -h output_hmmreport -f output_fasta sample1.fasta I do now get a output_gff file. However, it is simply empty. My sample1.fasta is just a .fasta file containing reordered contigs. I find it surprising that there would be no tsu/ssu/lsu output at all for this sample (and I tried on several other samples and got the same blank output_gff file. Any ideas why this may be happening (and is it because it cannot be run on Mac, which is the only OS I can currently download programs to?)

[Jianyu]

Sorry, due to the platform you used is not what the program expected, It is very hard to find out what was the cause. I strongly recommend you to run it on linux system to see what will happen