Question: Rnammer Gives Mysterious Error
0
gravatar for Lee Katz
6.2 years ago by
Lee Katz2.8k
Atlanta, GA
Lee Katz2.8k wrote:

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.

error • 2.9k views
ADD COMMENTlink modified 11 days ago by rosenkranz0 • written 6.2 years ago by Lee Katz2.8k

$HMMSEARCH_BINARY wasn't set, nevermind...

ADD REPLYlink written 6.2 years ago by Lee Katz2.8k
2
gravatar for jjjscuedu
4.8 years ago by
jjjscuedu30
jjjscuedu30 wrote:

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

ADD COMMENTlink written 4.8 years ago by jjjscuedu30
1
gravatar for Lee Katz
6.2 years ago by
Lee Katz2.8k
Atlanta, GA
Lee Katz2.8k wrote:

$HMMSEARCH_BINARY wasn't set, nevermind...

ADD COMMENTlink written 6.2 years ago by Lee Katz2.8k
0
gravatar for rosenkranz
11 days ago by
rosenkranz0
rosenkranz0 wrote:

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

ADD COMMENTlink written 11 days ago by rosenkranz0
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