diff --git a/build_pop.py b/build_pop.py
index 1ea4a0b0352ec8c20d30ae65c9cb92238971e51a..795de2692ede285b48992131cbceca82be056ebe 100755
--- a/build_pop.py
+++ b/build_pop.py
@@ -465,7 +465,7 @@ def generate_samples_fastq(haploid, nb_inds, output_dir, coverage, read_len, ins
                         stderr=open(stderr, "a") if stderr is not None else None)
 
 
-def confirm(deletions: dict, inversions: dict, variants: dict, printer: Print):
+def confirm(deletions: dict, inversions: dict, variants: dict, printer: Print, ask=True):
     # Deletions:
     nb_dels = 0
     variants_del = sorted(variants["DEL"], key=lambda x: x["min"])
@@ -521,7 +521,9 @@ def confirm(deletions: dict, inversions: dict, variants: dict, printer: Print):
     printer.out("")
 
     # Confirm:
-    return input("Continue [Y/n]? ") in ["y", "Y", ""]
+    if ask:
+        return input("Continue [Y/n]? ") in ["y", "Y", ""]
+    return True
 
 
 def init(output_dir, force_outputdir, sv_list, nstretches, nb_inds, reference, proba_del, proba_inv, haploid,
@@ -599,32 +601,40 @@ def init(output_dir, force_outputdir, sv_list, nstretches, nb_inds, reference, p
         except Exception:
             printer.err(traceback.format_exc())
             return 1
-    if quiet or genotypes is not None or confirm(deletions, inversions, sv_sim.variants, printer):
-        try:
-            if genotypes is None:
-                printer.out("GENERATE SUMMARY VCF FILE...\n")
-                genotypes_for_inds_DEL, genotypes_for_inds_INV = \
-                    build_genotypes_vcf_list(deletions, inversions, output_vcf, haploid, force_polymorphism, nb_inds,
-                                             tmp_dir, prg_path)
-            else:
-                nb_inds, genotypes_for_inds_DEL, genotypes_for_inds_INV = load_genotypes_from_file(genotypes)
-                if nb_inds < 2:
-                    printer.err("nb-inds must be at least 2")
-                    return 1
-            build_fastas_chromosomes(reference, genotypes_for_inds_DEL, genotypes_for_inds_INV, haploid, output_dir,
-                                     nb_inds, printer)
-            printer.out("GENERATE RANDOM READS FOR EACH INDIVIDUAL FROM GENOME...\n")
-            generate_samples_fastq(haploid, nb_inds, output_dir, coverage, read_len, insert_len_mean,
-                                   insert_len_sd, prg_path, threads, stdout, stderr)
-            printer.out("DONE!\n")
-        except ExecException as e:
-            printer.err(e)
-            return 1
-        except Exception:
-            printer.err(traceback.format_exc())
-            return 1
-    else:
-        printer.out("Aborted!\n")
+    if genotypes is not None:
+        printer_confirm = printer
+        if quiet:
+            with open(os.path.join(output_dir, "confirm.txt"), "w") as log_file:
+                printer_confirm = Print(stdout=log_file, stderr=stderr)
+                ok = confirm(deletions, inversions, sv_sim.variants, printer_confirm, False)
+        else:
+            ok = confirm(deletions, inversions, sv_sim.variants, printer_confirm)
+        if ok:
+            try:
+                if genotypes is None:
+                    printer.out("GENERATE SUMMARY VCF FILE...\n")
+                    genotypes_for_inds_DEL, genotypes_for_inds_INV = \
+                        build_genotypes_vcf_list(deletions, inversions, output_vcf, haploid, force_polymorphism, nb_inds,
+                                                 tmp_dir, prg_path)
+                else:
+                    nb_inds, genotypes_for_inds_DEL, genotypes_for_inds_INV = load_genotypes_from_file(genotypes)
+                    if nb_inds < 2:
+                        printer.err("nb-inds must be at least 2")
+                        return 1
+                build_fastas_chromosomes(reference, genotypes_for_inds_DEL, genotypes_for_inds_INV, haploid, output_dir,
+                                         nb_inds, printer)
+                printer.out("GENERATE RANDOM READS FOR EACH INDIVIDUAL FROM GENOME...\n")
+                generate_samples_fastq(haploid, nb_inds, output_dir, coverage, read_len, insert_len_mean,
+                                       insert_len_sd, prg_path, threads, stdout, stderr)
+                printer.out("DONE!\n")
+            except ExecException as e:
+                printer.err(e)
+                return 1
+            except Exception:
+                printer.err(traceback.format_exc())
+                return 1
+        else:
+            printer.out("Aborted!\n")
     return 0