Installation of rnammer-1.2 for Trinnoate: which version Perl XML/Simple.pm is required

Gwilym Haynes

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Feb 19, 2016, 3:18:37 PM2/19/16

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Hi Trinity community,

I am working on step 6. Running RNAMMER to identify rRNA transcripts of the Trinnoate protocol detailed on https://trinotate.github.io/ . Getting rnammer to work properly has been problematic, I suspect because the most recent version of the program was released in 2006 and is not compatible with the newer versions of Perl installed on our cluster.

Specifically, the program has not been able to find the module XML/Simple.pm. An example of the error messages is below:

Can't locate XML/Simple.pm in @INC (@INC contains:
/usr/local/globus/lib/perl
//global/software/perlbrew
//perls/perl-5.14.4/lib/site_perl/5.14.4/x86_64-linux
//global/software/perlbrew//perls/perl-5.14.4/lib/site_perl/5.14.4
//global/software/perlbrew//perls/perl-5.14.4/lib/5.14.4/x86_64-linux
//global/software/perlbrew//perls/perl-5.14.4/lib/5.14.4 .) at
/lustre/home/gwilymh/src/rnammer-1.2/xml2gff line 4. <-- NB: I added EOL characters here to make the error message easier to read

BEGIN failed--compilation aborted at /filepath/src/rnammer-1.2/xml2gff line 4.
error converting xml into gff
Error, cmd: perl /filepath/src/rnammer-1.2/rnammer -S euk -m tsu,lsu,ssu -gff tmp.superscaff.rnammer.gff < transcriptSuperScaffold.fasta died with ret 256 at /global/software/trinotate/Trinotate-2.0.2/util/rnammer_support/RnammerTranscriptome.pl line 80.

Does anyone know which version of Perl rnammer was developed to work with? Or has anyone encountered and worked around a similar problem?

Will Holtz

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Feb 19, 2016, 3:26:00 PM2/19/16

to Gwilym Haynes, trinityrnaseq-users

Have you tried to install XML::Simple with something like:
cpan install XML::Simple

-Will

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Gwilym Haynes

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Feb 19, 2016, 5:15:15 PM2/19/16

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Thanks Will,

One of the sys administrators installed the module for 'application/perl/5.14.4' (the only perl version installed on the cluster). The rnammer now produces a different error. Command:

/filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/RnammerTranscriptome.pl --transcriptome ${INPUT_FA} --path_to_rnammer /filepath/src/rnammer-1.2/rnammer

Returns:

Loading application/perl/5.14.4 module
CMD: /filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/util/superScaffoldGenerator.pl /filepath/RNASeq_P_miniata/All_Libraries_Transcriptome_Assembly/Trinity/Pmin_allLibraries.Trinity.fasta transcriptSuperScaffold 100
acc: TRINITY_DN79231_c0_g2_i1

Done.

CMD: perl /filepath/src/rnammer-1.2/rnammer -S euk -m tsu,lsu,ssu -gff tmp.superscaff.rnammer.gff < transcriptSuperScaffold.fasta
CMD: /filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl -R tmp.superscaff.rnammer.gff -T transcriptSuperScaffold.bed > Pmin_allLibraries.Trinity.fasta.rnammer.gff
WARNING: No RNAMMER features are described in file: tmp.superscaff.rnammer.gff at /filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl line 46.
Error, cmd: /filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl -R tmp.superscaff.rnammer.gff -T transcriptSuperScaffold.bed > Pmin_allLibraries.Trinity.fasta.rnammer.gff died with ret 65280 at /filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/RnammerTranscriptome.pl line 80.

... and the following files in the working directory:

transcriptSuperScaffold.bed 33.4 MB
Pmin_allLibraries.Trinity.fasta.rnammer.gff 0 B
tmp.superscaff.rnammer.gff 396 B ← died here?
transcriptSuperScaffold.fasta 281.2 MB

It seems to be trying to make a temporary file in filepath/trinotate/Trinotate-2.0.2/util/rnammer_support/util/, a directory that I do not have admin privileges in. Any suggestions?

Brian Haas

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Feb 19, 2016, 7:14:55 PM2/19/16

to Gwilym Haynes, trinityrnaseq-users

Hi Gwilym,

Rnammer can be tricky to set up. Be sure to run it's own test / sample data through to ensure that it's working before trying to run it on your own data via the Trinotate script.

best,

~brian

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