PHRED_PARAMETER_FILE=/opt/local/phred/PhredPar/phredpar.dat; export PHRED_PARAMETER_FILE; /opt/local/phred/phred -id /amino/gly/genomeD/snps/plates/ -trim_alt "" -sa /amino/gly/genomeD/snps/downloads/plates/.fasta -qa /amino/gly/genomeD/snps/downloads/plates/.fasta.qual -qr /amino/gly/genomeD/snps/downloads/plates/.fasta.hist&