use instead of require
chmod 755 to format_sra.pl
somehow we lost a /
add a protein flag
aTRAM should return nonzero status if there are no contigs made.
if a second parameter is passed to system_call, don't just exit, return the exit value.
if aTRAM returns no contigs, move on to the next sample.
if the sequence is a protein, use blastx to check bitscore instead of blastn.
use the complete.fasta file if it's available so that we don't waste so much time on alignments.
only use complete flag if specified.
complete_flag, not complete
Merge branch 'master' into configuration

Conflicts:
	format_sra.pl