I recently tried to user rnammer.
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).
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.
