set threads to 1 for hmmsearch, removed old commented code

scripts/search_ccms_all.py

@@ -75,7 +75,7 @@ def main():
                        '--noali',
                        '-T', HMMER_VAL_T,
                        '--domE', HMMER_VAL_DOME,
-                       #'--cpu', HMMER_VAL_CPU,
+                       '--cpu', HMMER_VAL_CPU,
                        '--domtblout', f'{temp_dir}/{args[ACC_ID]}.ccms.domtblout',
                        args[CCMS_PATH], args[FASTA_PATH] ]
     hmmsearch_cmd = ' '.join(hmmsearch_args)
@@ -84,8 +84,6 @@ def main():
         if hmmsearch != 0: # hmmsearch did not run successfully
             eprint(f'[{script_name}] error running: {hmmsearch_cmd}')
             return 2
-        #hmmsearch = subprocess.Popen(hmmsearch_args, stdout=DEVNULL) # stdout=subprocess.PIPE)
-        #hmmsearch.wait()
 
     modTax = {}
     with open(args[MODLIST_PATH],'r') as listFile:

scripts/search_hmm.py

@@ -12,6 +12,7 @@ script_name = os.path.splitext( os.path.basename(__file__) )[0]
 HMMER_PROG           = "hmmsearch"
 HMMER_VAL_T          = "0" # -T
 HMMER_VAL_DOME       = "1" # -domE
+HMMER_VAL_CPU        = "1" # --cpu
 PROTEIN_ID           = 'HMMer-3'
 TAXON                = 'ALL'
 
@@ -75,7 +76,7 @@ def main():
                        '--noali',
                        '-T', HMMER_VAL_T,
                        '--domE', HMMER_VAL_DOME,
-                       #'-o', '{path}/{outprefix}.out'.format(path=temp_dir,outprefix=args[ACC_ID]),
+                       '--cpu', HMMER_VAL_CPU,
                        '--domtblout', f'{temp_dir}/{args[ACC_ID]}.domtblout',
                        args[HMM_PATH], args[FASTA_PATH] ]
     hmmsearch_cmd = ' '.join(hmmsearch_args)
@@ -85,13 +86,6 @@ def main():
             eprint(f'[{script_name}] error running: {hmmsearch_cmd}')
             return 1
 
-    # compute HMMs alignment identities
-    #percentIden = {}
-    #with open('{path}/{outprefix}.out'.format(path=temp_dir,outprefix=args[ACC_ID]), 'r') as resAlignFile:
-    #    iterHMMRes = hmmer_align_iter(resAlignFile)
-    #    for seq,start,end,countPos in iterHMMRes:
-    #        percentIden["{0}_{1}_{2}".format(seq,int(start),int(end))] = countPos
-
     # write result files
     with open(f'{results_dir}/{args[ACC_ID]}.hmm.res','w') as outFile, open(f'{temp_dir}/{args[ACC_ID]}.domtblout','r') as resFile:
         for line in resFile: