I would like to use Pseudopipe. But I have been having some problems while executing PseudoPipe. To test the program I used the example input files (from Caenorhabditis Elegans) which were given. I modified the env.sh. I indicated the paths to python (python2.7), blast (blastall 2.2.25) and tfasty (tfasty36). But no pseudogenes were found when I executed the command which is shown below. I added a screenshot of the error as attachment. Could you give me some guidance to solve this problem?
The command that I am using is:
./pseudopipe.sh ~/pgenes/ppipe_output/caenorhabditis_elegans_62_220a ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.I.fa ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chrI_exLocs 0
I downloaded PseudoPipe from:
The reason you are not getting any output is because you need to use fasta-35.1.5 (tfasty35). The newer versions of the fasta (e.g. tfasty36) have a different output format that cannot be processed by the downstream programs in our pipeline. We are currently working on updating and improving the pipeline, but for the time being please do use tfasty35.