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  • transdecoder

    Hi,
    Has anyone used Transdecoder from trinotate (Trinity denovo assembly).
    Here is my problem. I using transdecoder for gene ontology of assembled contigs. When I run Transdecoder with the following command

    transdecoder_rel16JAN2014]$ TransDecoder -t /xxxyyy/Trinity.fasta --search_pfam /xxxyyyzzz/Pfam-A.hmm --prepare_pfam

    I get the following

    We have prepared the transdecoder.tmp.13987/parafly.sh command file for you to run hmmscan separately (e.g. on a cluster).
    Example for a single node with 2 CPUs :
    ParaFly -CPU 2 -c transdecoder.tmp.13987/parafly.sh --failed transdecoder.tmp.13987/parafly.sh.failed -vv

    After your PFAM searches are complete, then concatanate all the out.db files using this command into transdecoder.tmp.13987/longest_orfs.pep.pfam.out.
    cat transdecoder.tmp.13987/*.out.db|tr -d '\000' |grep -v '^#' > transdecoder.tmp.13987/longest_orfs.pep.pfam.out

    Then in order to restart transdecoder use the following command (along with any other options you want):
    /xxxyyy/pfam_runner.pl --pep transdecoder.tmp.13987/longest_orfs.pep --search_pfam /xxxyyyzzz/Pfam-A.hmm --pfam_out transdecoder.tmp.13987/longest_orfs.pep.pfam.out --reuse --workdir transdecoder.tmp.13987

    But when I run
    transdecoder.tmp.13987/parafly.sh --failed transdecoder.tmp.13987/parafly.sh.failed -vv

    I dont get any out.db file generated.

    Can some please tell what am i missing?

    Thanks
    Regards
    Vishwesh

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