Trinotate - superScaffoldGenerator.pl has wrong path

[mictadlo]

Hi @jerowe and @lecorguille, I got the below error running Trinotate:

CMD: /mnt/apps/miniconda2/bin/util/superScaffoldGenerator.pl ../trinotate/smsk_trinotate.bak/Trinty_PE_all_Assembled_Transcripts.fasta transcriptSuperScaffold 100
Can't exec "/mnt/apps/miniconda2/bin/util/superScaffoldGenerator.pl": No such file or directory at /mnt/apps/miniconda2/bin/RnammerTranscriptome.pl line 81.
Error, cmd: /mnt/apps/miniconda2/bin/util/superScaffoldGenerator.pl ../trinotate/smsk_trinotate.bak/Trinty_PE_all_Assembled_Transcripts.fasta transcriptSuperScaffold 100 died with ret -1 at /mnt/apps/miniconda2/bin/RnammerTranscriptome.pl line 83.
ubuntu@waterhouse-1:/scratch/tmp$ superScaffoldGenerator.pl
usage: /mnt/apps/miniconda2/bin/superScaffoldGenerator.pl fasta_file output_prefix gapLength

This is the following solution is to remove util from the $cmd path:

miniconda2/bin/RnammerTranscriptome.pl
    my $cmd = "$FindBin::RealBin/util/superScaffoldGenerator.pl $transcriptome_fasta transcriptSuperScaffold 100";
    $cmd = "$FindBin::RealBin/util/rnammer_supperscaffold_gff_to_indiv_transcripts.pl -R tmp.superscaff.rnammer.gff -T transcriptSuperScaffold.bed > $output_file";

Please change them to

    my $cmd = "$FindBin::RealBin/superScaffoldGenerator.pl $transcriptome_fasta transcriptSuperScaffold 100";
    $cmd = "$FindBin::RealBin/rnammer_supperscaffold_gff_to_indiv_transcripts.pl -R tmp.superscaff.rnammer.gff -T transcriptSuperScaffold.bed > $output_file";

Thank you in advance.

Michal

[sk-sahu]

Is this got solved in the latest version of bioconda-recipes?

Because I am also getting the same issue with autoTrinotate.pl

[rwhetten]

A new installation of the Trinotate package from bioconda still has the same problem. Is there any plan to fix this?