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diff --git a/__pycache__/merging.cpython-36.pyc b/__pycache__/merging.cpython-36.pyc
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diff --git a/__pycache__/splitReads.cpython-36.pyc b/__pycache__/splitReads.cpython-36.pyc
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diff --git a/globalVars.py b/globalVars.py
index 32c75caa0d54cff2b04db8895bb1019f783c314d..dda5a3d55304f81299004155a8517189f601a8a2 100644
--- a/globalVars.py
+++ b/globalVars.py
@@ -199,12 +199,11 @@ class mySCAF:
 
 
 # function to initialize global variables
-def init(out, sL, mL, mO, mI, t, mSV, bPATH, mPATH):
+def init(out, sL, mL, mO, mI, t, mSV):
     global largestContig, distError, outDir, splitLen, minOverlap, minLinks
     global minIdent, threads, contsMerged, contLenDICT, contDICT, mergedDICT, readHash
     global contigGR, adjustDICT, gapDICT, eDICT, edgeDICT
     global blastCounter, poserrorHASH, minSVL
-    global blastP, minimap2P 
 
     global insE, delE, invE, mjE, goodE
     insE={}
diff --git a/main.py b/main.py
index 83ed55f67074140868c845666eeedf40d6a212c4..a3cb7b756f9ec638ce8c5b3207c65727066d804e 100755
--- a/main.py
+++ b/main.py
@@ -74,31 +74,7 @@ class mySCAF:
 ###functions#######################
 ###################################
 
-# function to parse the config file containing the paths to
-# blastn and minimap2
-def parsePATHs():
-    scriptPath=sys.argv[0].rstrip("main.py")
-    configReader=open("%s/config.txt"%scriptPath)
-    minimap2Path=""
-    blastnPath=""
-    for line in configReader:
-        if not line.startswith("#"):
-            if line.startswith("MINIMAP2"):
-                minimap2Path = line.strip().split("=")[-1]
-            elif line.startswith("BLASTN="):
-                blastnPath = line.strip().split("=")[-1]
-    if minimap2Path=="":
-        print("Error no entry for minimap2 path in config.txt found - exiting...")
-        exit()
-    if blastnPath=="":
-        print("Error no entry for blastn path in config.txt found - exiting...")
-        exit()
-    configReader.close()
-    #print("minimap path: %s"%(minimap2Path))
-    #print("blastn path: %s"%(blastnPath))
-    
-    return minimap2Path, blastnPath
-    
+ 
 #function to reverse complement a sequence
 def reverseComplement(seq):
     old = "ACGT"
@@ -110,9 +86,7 @@ def runMinimap2(nThreads, mapMode, inFA, inFQ, outPAF):
     scriptPath=sys.argv[0].rstrip("main.py")
     try:
         subprocess.call("%s/minimap2/minimap2 -t %i -x %s %s %s> %s" %
-                        (scriptPath, nThreads, mapMode, inFA, inFQ, outPAF), shell=True, stdout=DEVNULL, stderr=subprocess.STDOUT)
-        #subprocess.call("%s/minimap2/minimap2 -t %i -x %s %s %s> %s" %
-        #                (scriptPath, nThreads, mapMode, inFA, inFQ, outPAF), shell=True)
+                        (scriptPath, nThreads, mapMode, inFA, inFQ, outPAF), shell=True, stdout=DEVNULL)
     except:
         print("Problem running minimap2 - check if its properly set up")
 
@@ -800,13 +774,11 @@ def removeTMPfiles():
 def run(genome, nobreak, curIter):
     # create output directory if it not exists already
     subprocess.call("mkdir -p %s" % (args.outdir), shell=True)
-    
-    miniPATH, blPATH = parsePATHs()
 
     # initlaiye global variables
     if curIter > 0:
         tempStore=globalVars.readHash
-    globalVars.init(args.outdir, args.size, args.minlinks, args.minoverlap, args.minident, args.threads, args.minSVLen, blPATH, miniPATH)
+    globalVars.init(args.outdir, args.size, args.minlinks, args.minoverlap, args.minident, args.threads, args.minSVLen)
     
     if curIter>0:
         globalVars.readHash=tempStore