===== setting up environment variables =====
using Athaliana matrix
will run Augustus_evidence: Augustus
will run GeneWise_SplicePredictor: GeneWise;SplicePredictor
[19:22:14] ########## Starting pipeline ##########
[19:22:14] ##### Stage 1 [Pre-processing] #####
[19:22:14] creating symlink to: 01_refseq.fas
[19:22:15] translating sequences in 6 reading frames
[19:22:16] extracting ORFs from translated genomic sequence
[19:22:22] creating symlink to: 51_gene.gff
gff2gtb.pl -i 51_gene.gff -o 61_gene.gtb
Can't exec "gff2gtb.pl": Permission denied at /zeus04/data/woog3/mike/SPADA/SPADA-master/Common.pm line 103.
Failed: Permission denied