[Transdecoder-users] Transdecoder help: failure to output final .pep files

[Edward G. <e.g...@im...>]

Hello

I've been trying to run Transdecoder with pfam searching on transcriptome assemblies that I made using Soapdenovo-Trans(SdT). With different assemblies and different PBS parameters (like where I place the data on our system's parallel shared file system etc), Transdecoder creates the temp directory with some of the intermediate files. No finished output files are ever produced. Once I got the .dat file with the pfam hits for my assembly but there were no final .pep .gff3 .cds or .bed files produced and stored anywhere. Am I missing something?

Unlike Trinity, SdT plugs in Ns if there is an expected gap between the fragments of a transcript. Could these Ns be tripping up Transdecoder?

NOTES:
My scripts load the modules our system operators made for Transdecoder and hmmer before sending commands for Transdecoder.

These are example entries from my input fasta:

>centroid=Fi49merScaf_11503;seqs=3;
AACTAAGGGTTTGTTGCTTTTATCAGCGAAATATATTAATGTTTTTAAATTATAGTTGACAACTTTACCGATGAACTATTGAGGTACAGCTTTTTGGGAACATATAGTCTAGTGCCAAGTCCTTCTAGTGCTTTCACACACTCGGCAATACTCTCTTCACTATCAATGTCCATGTTCCAAATTGCCGC...
>centroid=Fi49merScaf_29126;seqs=1;
TTGGCTGAGAGAACTTACACAAGCCACTTATCGAGCTTCTGCCCCTCCGCCCATCAACATACTTGGAGAACTAAGCAATGATGTAGCGGAAACTGCTGAACCTAGAGCTGTAAATGCTAGGACAGCGGATCTTGTTGTTAATGGAACACTGATTGAGATGAAGTTATCATTATATGTGAAGG...
centroid=Fi49merScaf_29118;seqs=1;
CTGACATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCAAATAGACTGTACAGCATTATAGACAGGTACCTCACAGACTTAAAAAGCCCTTAAGACTGTTTTCCTGTAAAAGAATCTCCTTTTTTAACACAGAAATTATCTACAAAATCTAATTCGGAGACCACGGTGTTAACCAAATC...


Thanks
Ed

Dr. Edward K Gilding

The Institute of Molecular Biosciences
The University of Queensland
Brisbane, QLD 4072
Australia

O: +61 07 3346 2014