diff --git a/cnvpipelines.py b/cnvpipelines.py
index 022472450405e095498c250908e984eb91e8945a..ca3317293457acbc46c21a6c06d181772d336ae2 100755
--- a/cnvpipelines.py
+++ b/cnvpipelines.py
@@ -118,13 +118,13 @@ class CnvPipeline:
 
                 # Some checks:
                 if not os.path.isfile(sample):
-                    raise ValueError("Sample file '%s' does not exists" % sample)
+                    raise ValueError("Sample bam file '%s' does not exists" % sample)
                 bam = pysam.AlignmentFile(sample)
                 if "RG" not in bam.header:
-                    raise ValueError("Sample file '%s' has no RG tag in headers" % sample)
+                    raise ValueError("Sample bam file '%s' has no RG tag in headers" % sample)
                 samples_list = bam.header['RG']
                 if len(samples_list) == 0:
-                    raise ValueError("Sample file '%s' has none sample" % sample)
+                    raise ValueError("Sample bam file '%s' empty read group (RG) list" % sample)
 
                 # Get sample name:
                 if len(samples_list) > 1:
@@ -171,10 +171,10 @@ class CnvPipeline:
 
             if len(samples_name) > 0: ## Sample names for the batch
                 self._write_samples(samples_name, smple_file + "." + str(n_block))
-                
+
             if len(all_samples_name) > 0: ## All samples names
-                self._write_samples(all_samples_name, smple_file)    
-            
+                self._write_samples(all_samples_name, smple_file)
+
 
     @staticmethod
     def _fail(message):
@@ -649,7 +649,7 @@ class CnvPipeline:
 
     def run_detection(self, reference, tools, samples, variant_types, chromosomes="all", force_wdir=False, batches=-1,
                       batches_parallel=5, refbundle=None, force_all_chr=False, **kwargs):
-        
+
         print("rundetection",self, reference, tools, samples, variant_types, chromosomes="all", force_wdir=False, batches=-1,batches_parallel=5, refbundle=None, force_all_chr=False, **kwargs)
         """
         Run a detection workflow
@@ -1128,7 +1128,7 @@ class CnvPipeline:
             # Create sample file for fastq files:
             samples_file_fq = os.path.join(self.wdir, "samples.yml")
             samples_file_d = os.path.join(self.wdir, "samples.list")
-            
+
             self._create_samples_fastq_simulaton(nb_inds, samples_file_fq)
             self._create_samples_detection_simulation(nb_inds, samples_file_d)
 
@@ -1533,7 +1533,7 @@ if __name__ == "__main__":
     test_parser.set_defaults(func="run_test")
 
     args = parser.parse_args()
-    
+
 
 
     if args.func == "run_detection" and args.refbundle is None and "genomestrip" in args.tools:
diff --git a/snakecnv/align.snk b/snakecnv/align.snk
index d8067cc7b08c64257b3172d2a7698540586f6a5e..f634d623a0fe070da9e9d7b34ca54939c64b369a 100644
--- a/snakecnv/align.snk
+++ b/snakecnv/align.snk
@@ -48,7 +48,7 @@ rule bwamap:
     output:
         bam = temp("bwa/{sample}.bam")
     threads:
-        get_threads("bwamap", 4)
+        get_threads("bwamap", 8)
     log:
         stdout = "logs/map_{sample}.o",
         stderr = "logs/map_{sample}.e"
@@ -91,4 +91,4 @@ rule markduplicate:
         """
         picard MarkDuplicates I={input.bam} O={output.bam} M={output.metrics} REMOVE_DUPLICATES=true 1> {log.stdout} \
         2> {log.stderr};
-        """
\ No newline at end of file
+        """
diff --git a/snakecnv/bin/findNstretches.py b/snakecnv/bin/findNstretches.py
index 7a5b7a36c2b405f383354d81a980be74bfddb44c..b18025168b105a846df411d2a8c61813ab49430a 100755
--- a/snakecnv/bin/findNstretches.py
+++ b/snakecnv/bin/findNstretches.py
@@ -24,7 +24,7 @@ def find_chrom_Nstretches(chrom, fastafile, cutoff):
     p = re.compile("N{%s,}" % cutoff)
     with FastaFile(fastafile) as fasta:
         sequence = fasta.fetch(chrom)
-        gaps = [(chrom, m.start(), m.end() + 1) for m in re.finditer(p, sequence)]
+        gaps = [(chrom, m.start(), m.end()) for m in re.finditer(p, sequence)]
     return gaps