transdecoder

[vishwesh]

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