When the input file is in the current working directory, and -o is specified, the input file gets moved

[wwood]

I guess it is due to this part of the code (the mv)

# HMM aligning
def hmmalign(hmm, sequencefile):
    base_name = replace_name(sequencefile, '')  # Create a base name for output files
    subprocess.check_call("mkdir -p " + cl.o[0], shell=True)
    subprocess.check_call("mv " + base_name + ".* " + cl.o[0], shell=True)
    subprocess.check_call('hmmalign --trim -o ' + base_name + '.sto ' + hmm + ' ' + cl.o[0] + '/' + sequencefile, shell=True)
    subprocess.check_call('seqmagick convert ' + base_name + '.sto ' + base_name + '_conv_.fa', shell=True)

[geronimp]

Fixed