diff --git a/viloca/shotgun.py b/viloca/shotgun.py
index 26eccbe..45c34e4 100644
--- a/viloca/shotgun.py
+++ b/viloca/shotgun.py
@@ -120,7 +120,7 @@ def parse_aligned_reads(reads_file):
         # end index of the aligned read w.r.t reference (1-based indexing)
         out_reads[name][3] = int(mstop)
         out_reads[name][4] = this_m
-    handle.close()
+
     return out_reads
 
 
@@ -311,7 +311,7 @@ def win_to_run(alpha_w, seed, inference_type, n_max_haplotypes, n_mfa_starts, un
         if not os.path.isfile(output_name):
             j = min(300_000, int(cov) * 15)
             rn_list.append((winFile, j, alpha_w, seed, inference_type, n_max_haplotypes, n_mfa_starts, unique_modus, inference_convergence_threshold))
-    file1.close()
+
     del end
     del(beg, chr1)
     return rn_list