Rnammer Gives Mysterious Error

Question

[Lee Katz]

Does anyone have experience with RNAmmer? On my new machine it gives an error after running it every time. I have tried to edit the file to understand it better and so the error message might be slightly different than yours. I altered SIG{INT} to produce a line number, and the line number could be a couple of lines off due to the SIG{INT} code. I would appreciate any insight into the error, as the authors are not returning my email...

[lkatz@localhost cholerae]$ rnammer -S bac -multi -m tsu,lsu,ssu -gff tmp/build/prediction/rnammer.gff -xml tmp/build/prediction/rnammer.xml -f tmp/build/prediction/rnammer.ffn tmp/assembly.fasta
/home/lkatz/bin/rnammer/rnammer: main::fault_exit:
/home/lkatz/bin/rnammer/rnammer: main::fault_exit:
/home/lkatz/bin/rnammer/rnammer: main::fault_exit:
/home/lkatz/bin/rnammer/rnammer: : Could not open temp file './25729.lsu.xml' for reading: No such file or directory at /home/lkatz/bin/rnammer/rnammer line 223, <> line 4382.
[lkatz@localhost cholerae]$ ls
25729.lsu.cf  25729.tsu.cf  temp.25729.fsa  tmp
25729.ssu.cf  temp.25729.xml

Some insight: 4382 is the number of lines in my fasta input.

[Lee Katz]

$HMMSEARCH_BINARY wasn't set, nevermind...

Answer 1

[jjjscuedu]

I also have problems about rnammer running:

I have edited the path of rnammer like this:

the path of the program

my $INSTALL_PATH = "/home/jingjing/software/rnammer";

The library in which HMMs can be found

my $HMMLIBRARY = "$INSTALLPATH/lib"; my $XML2GFF = "$INSTALLPATH/xml2gff"; my $XML2FSA = "$INSTALLPATH/xml2fsa";

The location of the RNAmmer core module

my $RNAMMERCORE = "$INSTALLPATH/core-rnammer";

path to hmmsearch of HMMER package

chomp ( my $uname = uname); my $HMMSEARCHBINARY; my $PERL; if ( $uname eq "Linux" ) { $HMMSEARCHBINARY = "/home/jingjing/software/hmmer-3.0-linux-intel-x8664/binaries/hmmsearch"; $PERL = "/usr/bin/perl"; } elsif ( $uname eq "IRIX64" ) { $HMMSEARCHBINARY = "/home/jingjing/software/hmmer-3.0-linux-intel-x86_64/binaries/hmmsearch"; $PERL = "/usr/sbin/perl"; } else { die "unknown platform\n"; }

However, when I try to run on the example data: perl rnammer -S bac -m lsu,ssu,tsu -gff test.gff -xml test.xml -f test.fasta -h test_resport.txt example/ecoli.fsa

There is nothing in the report file and no rRNA result in the gff file.

Do you know where I am wrong?

Thanks!

Jingjing

Answer 2

[rosenkranz]

Don't know if this is still interesting but after fixing lot of problems I finally managed to run RNAmmer 1.2.

There is a strange part in the rnammer Perl script that looks like this:

chomp ( my $uname = `uname`);
my $HMMSEARCH_BINARY;
my $PERL;
if ( $uname eq "Linux" ) {
    $HMMSEARCH_BINARY = "/usr/cbs/bio/bin/linux64/hmmsearch";
    $PERL = "/usr/bin/perl";
} elsif ( $uname eq "IRIX64" ) {
    $HMMSEARCH_BINARY = "/usr/cbs/bio/bin/irix64/hmmsearch";
    $PERL = "/usr/sbin/perl";
} else {
    die "unknown platform\n";
}

This code will not work since these paths do not exist. I replaced the upper code by the following:

my $HMMSEARCH_BINARY = "/home/myname/Desktop/hmmer/hmmsearch";
my $PERL = "/usr/sbin/perl";

I downloaded the latest binaries of hmmer (3.1.b2) and coppied the executable file 'hmmsearch' into the directory stated above. However, rnammer still did not output any results. After removing a code line in the core-rnammer script that deletes temporary files I found that hmmsearch (which is called from within the core-rnammer script) quits with an error: unknown option --compat. Obviosly, this option is no longer supported in the current hmmer version. Thus, I downloaded an older version (2.2g), compiled the source code and replaced the hmmersearch binary by the newly compiled one.

... and it worked

[JackAttack]

THANK YOU! I had the same issue with no output so downloaded hmmer v2.2g and now rnammer-1.2 works. Thanks for the tip!

Answer 3

[Lee Katz]

$HMMSEARCH_BINARY wasn't set, nevermind...