error to run rnammer

Question

[microorganism_001]

I have installed rnammer software to extract 16s rRNA gene and dependencies (hammer) but I am getting errors when run it. I have followed many tutorials but they have not worked out please reply why it's not working thanks.

./rnammer -S bac -m ssu -gff output.gff -h hmm.out -f output.fna genomic.fna

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /home/omic/miniforge3/lib/perl5/5.32/site_perl /home/omic/miniforge3/lib/perl5/site_perl /home/omic/miniforge3/lib/perl5/5.32/vendor_perl /home/omic/miniforge3/lib/perl5/vendor_perl /home/omic/miniforge3/lib/perl5/5.32/core_perl /home/omic/miniforge3/lib/perl5/core_perl .) at /home/omic/Downloads/rnammer/xml2gff line 4.
BEGIN failed--compilation aborted at /home/omic/Downloads/rnammer/xml2gff line 4.
error converting xml into gff

Answer 1

[Mensur Dlakic]

please reply why it's not working thanks.

I don't think it can be any clearer than it already is.

FATAL: POSIX threads support is not compiled into HMMER; --cpu doesn't have any effect

What is unclear about that message? HMMer needs to be compiled differently than it already is to support threads. If you go to the HMMer website, there will be an explanation how to do it. Or you can download pre-compiled binaries.

Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module)

This also is as clear as it gets. Perl module XML::Simple is missing and needs to be installed. Googling about installing Perl modules will give you an answer, but I will get you going:

http://www.cpan.org/modules/INSTALL.html

[microorganism_001]

Thank you respected sir for your response but now I installed a pre-compiled binary and still getting an error sh: 1: /usr/share/man/man1/hmmsearch.1.gz: Permission denied

[Mensur Dlakic]

/usr/share/man/man1/hmmsearch.1.gz is not a binary file, but rather a file needed for the manual command. Don't know how you even came up with an idea to use that file, as the binary itself is called hmmsearch. You will have to point to a correct binary, and this is some basic stuff you need to figure out on your own.

[microorganism_001]

Sir, I took a shortcut I found the binary file from the miniforge conda package "home/omic/miniconda3/pkgs/hmmer-3.1b2-3/bin/hmmsearch" but now there is all the output I am getting as expected but all the files are blank and for a file only has structure looks like following for a gff file. I have tried for two different genomes but have not worked with the following command - "./rnammer -S bac -m ssu -gff output.gff -h hmm.out -f output.fna ecoli.fsa"

It is an output of gff file.

##gff-version2
##source-version RNAmmer-1.2
##date 2024-01-11
##Type DNA
# seqname           source                      feature     start      end   score   +/-  frame  attribute
# ---------------------------------------------------------------------------------------------------------
# ---------------------------------------------------------------------------------------------------------

[Mensur Dlakic]

I think your original problem has been solved. I don't have the capacity to go through detailed troubleshooting with you step by step, as there are all kinds of things that could have been done wrong, starting with how the program was installed. This is also a fairly old program that may not work properly on modern computer architectures.

You may want to consider SSU-ALIGN, which also does what you want and it may be easier to work with. Beware that it won't make a GFF output if that is something important to you.

[Mensur Dlakic]

It just occurred to me that rnammer may need older version (HMMER 2.3.2) rather than v3.1 that you seem to have. Those older versions should also be available as binaries from the HMMer site.

[microorganism_001]

Sir, I have tried everything for rnammer software but it doesn't work out installed 2.3.2, and installed precompiled binary as given process but does not work, always generates a blank file. I also tried SSU-ALIGN but this software can't fetch out 16s RNA. I want to fetch out only 16s rRNA and want to create a phylogenetic tree for multiple genomes. If it is possible through any means let me know.

[Mensur Dlakic]

With all due respect, both programs work fine but you are using them wrong. I just tried rnammer after a long time of not using it and it sill works fine. Same for SSU-ALIGN which most definitely will extract 16S rRNA sequences. From all the posts you made in other threads it would appear that you are not reading their manuals properly, and in particular that you may not have a basic background in installing programs (for HMMer) or following directions how to run a program in order to achieve a particular output (for SSU-ALLIGN). I already explained that I don't have the time to fix all your problems one at a time. But both programs work for what you need to do, and SSU-ALIGN would be my choice.

[microorganism_001]

Thank you, sir, for your contineous reply hmmer does work out finally.