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

    Hi Trinity community,

    I am working on step 6. Running RNAMMER to identify rRNA transcripts of the Trinoate 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?

    NB: I have posted this same question on the Trinity Google Groups forum: https://groups.google.com/forum/#!to...rs/BY8HsR0Rv8A
    Last edited by gwilymh; 02-19-2016, 12:22 PM. Reason: I left something out by mistake

  • #2
    Update: 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?
    Last edited by gwilymh; 02-19-2016, 02:38 PM.

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