ENH update error checking&doc

Author: cocodyq

README.md

@@ -14,8 +14,10 @@ Create conda environment(only support python v3.8/v3.9)
 
 ```bash
 conda create -n gmscmapper python=3.8
+conda activate gmscmapper
 or
 conda create -n gmscmapper python=3.9
+conda activate gmscmapper
 ```
 
 You will need the following dependencies:

gmsc_mapper/main.py

@@ -199,13 +199,13 @@ def expect_file(f):
                 sys.stderr.write("GMSC-mapper Error:The first two columns of output should be `query` and `target`.\n")
                 sys.exit(1)             
 
-    if args.habitat:
+    if not args.nohabitat and args.habitat:
         expect_file(args.habitat)
 
-    if args.taxonomy:
+    if not args.notaxonomy and args.taxonomy:
         expect_file(args.taxonomy)
 
-    if args.quality:
+    if not args.noquality and args.quality:
         expect_file(args.quality)
 
 def create_db(arguments):