diff --git a/modules/Runner.pm b/modules/Runner.pm
index 3c9795b..550d2f8 100644
--- a/modules/Runner.pm
+++ b/modules/Runner.pm
@@ -1120,7 +1120,7 @@ sub _get_temp_prefix
     my $dir  = $self->_get_temp_dir($fname);
     if ( ! -d $dir ) 
     { 
-        `mkdir -p $dir`; 
+        `mkdir -p '$dir'`;
         if ( $? ) { $self->throw("Cannot create directory [$dir]: $!"); }
     }
     return "$dir/$file";
@@ -1140,7 +1140,7 @@ sub _mkdir
 {
     my ($self,$fname) = @_;
     $fname =~ s{[^/]+$}{};
-    if ( !-e $fname ) { `mkdir -p $fname`; }
+    if ( !-e $fname ) { `mkdir -p '$fname'`; }
     return $fname;
 }
 
diff --git a/scripts/run-beagle b/scripts/run-beagle
index 99e24e0..aa639f0 100755
--- a/scripts/run-beagle
+++ b/scripts/run-beagle
@@ -266,7 +266,7 @@ sub mrProper
 sub runtime_stats
 {
     my ($self,$outfile) = @_;
-    $self->cmd("mkdir -p $outfile.part");
+    $self->cmd("mkdir -p '$outfile.part'");
     $self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
     rename("$outfile.part",$outfile) or $self->throw("rename $outfile.part $outfile: $!");
 }
@@ -473,7 +473,7 @@ sub beagle
 
     if ( !-e "$prefix.vcf.gz" or $$self{redo_beagle} )
     {
-        $self->cmd(qq[mkdir -p $outdir]);
+        $self->cmd(qq[mkdir -p '$outdir']);
         my $mem = int($self->get_limits('memory') * 0.8);
         if ( $mem<=0 ) { $mem = 500; }
         my $known = defined $known_vcf ? "ref=$known_vcf" : '';
@@ -576,7 +576,7 @@ sub save_config
     my $src = $$self{_config};
     my $dst = "$$self{outdir}/beagle.conf";
     if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
-    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
+    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
     open(my $fh,'>',$dst) or $self->throw("$dst: $!");
     my $about = $$self{_about};
     $about =~ s/\n/\n# /g;
diff --git a/scripts/run-bt-mpileup b/scripts/run-bt-mpileup
index 3a5dfc9..299bf6c 100755
--- a/scripts/run-bt-mpileup
+++ b/scripts/run-bt-mpileup
@@ -280,7 +280,7 @@ sub clean
 sub runtime_stats
 {
     my ($self,$outfile) = @_;
-    $self->cmd("mkdir -p $outfile.part");
+    $self->cmd("mkdir -p '$outfile.part'");
     $self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
     open(my $fh,'>',"$outfile.part/info.txt") or $self->throw("$outfile.part/info.txt: $!");
     print $fh $$self{_about};
@@ -294,7 +294,7 @@ sub save_config
     my $src = $$self{_config};
     my $dst = "$$self{outdir}/mpileup.conf";
     if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
-    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
+    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
     open(my $fh,'>',$dst) or $self->throw("$dst: $!");
     my $about = $$self{_about};
     $about =~ s/\n/\n# /g;
@@ -470,14 +470,14 @@ return;
     {
         if ( !exists($bam_pls{$pl}) ) { $self->throw("The platform \"$pl\" not present in any of the BAMs.\n"); }
     }
-    `mkdir -p $$self{outdir}`;
+    `mkdir -p '$$self{outdir}'`;
     $self->cmd("touch $$self{outdir}/sanity_checked");
 }
 
 sub open_file
 {
     my ($self,$file) = @_;
-    if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p $1"); }
+    if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p '$1'"); }
     open(my $fh,'>',$file) or $self->throw("$file: $!");
     return $fh;
 }
diff --git a/scripts/run-commands b/scripts/run-commands
index d54e1cf..8b8cc55 100755
--- a/scripts/run-commands
+++ b/scripts/run-commands
@@ -76,7 +76,7 @@ sub main
     $self->parse_args();
 
     my @files = $self->list_files($$self{glob});
-    `mkdir -p $$self{outdir}`;
+    `mkdir -p '$$self{outdir}'`;
 
     for my $file (@files)
     {
@@ -135,7 +135,7 @@ sub run_command
 {
     my ($self,$outfile,$file) = @_;
     my $tmpdir = "$$self{outdir}/tmp.$file";
-    $self->cmd("mkdir -p $tmpdir");
+    $self->cmd("mkdir -p '$tmpdir'");
     for my $cmd (@{$$self{cmds}})
     {
         my $task = $self->expand_task(cmd=>$cmd,name=>$file,tmpdir=>$tmpdir);
diff --git a/scripts/run-gvcf-calling b/scripts/run-gvcf-calling
index d723951..f4d13ce 100755
--- a/scripts/run-gvcf-calling
+++ b/scripts/run-gvcf-calling
@@ -138,7 +138,7 @@ sub main
     my $outdir = $$self{outdir};
     if ( $self->is_finished("$outdir/all_done") ) { $self->all_done; }
 
-    $self->cmd(qq[mkdir -p $outdir]);
+    $self->cmd(qq[mkdir -p '$outdir']);
     $self->save_config();
 
     my $chunks = $self->init_chunks();
@@ -223,7 +223,7 @@ sub clean
 sub runtime_stats
 {
     my ($self,$outfile) = @_;
-    $self->cmd("mkdir -p $outfile.part");
+    $self->cmd("mkdir -p '$outfile.part'");
     $self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
     open(my $fh,'>',"$outfile.part/info.txt") or $self->throw("$outfile.part/info.txt: $!");
     print $fh $$self{_about};
@@ -238,7 +238,7 @@ sub save_config
     my $src = $$self{_config};
     my $dst = "$$self{outdir}/mpileup.conf";
     if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
-    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
+    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
     open(my $fh,'>',$dst) or $self->throw("$dst: $!");
     my $about = $$self{_about};
     $about =~ s/\n/\n# /g;
diff --git a/scripts/run-impute2 b/scripts/run-impute2
index 525588c..63a7aeb 100755
--- a/scripts/run-impute2
+++ b/scripts/run-impute2
@@ -289,7 +289,7 @@ sub mrProper
 sub runtime_stats
 {
     my ($self,$outfile) = @_;
-    $self->cmd("mkdir -p $outfile.part");
+    $self->cmd("mkdir -p '$outfile.part'");
     $self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
     rename("$outfile.part",$outfile) or $self->throw("rename $outfile.part $outfile: $!");
 }
@@ -540,7 +540,7 @@ sub vcf_to_impute2
 
     if ( $$self{phased_only} ) { $self->throw("todo: phased_only"); }
 
-    $self->cmd(qq[mkdir -p $outdir]);
+    $self->cmd(qq[mkdir -p '$outdir']);
 
     if ( exists($$self{known_vcf}) && !$self->known_hapref_exists($chr,"$from-$to") )
     {
@@ -614,7 +614,7 @@ sub impute2
                 $knowns .= " -h $known${i}.hap.gz -l $known${i}.legend.gz";
             }
             my $rg_prefix = "$$self{known_hapref}/$chr/$from-$to.ref";
-            $self->cmd(qq[mkdir -p $$self{known_hapref}/$chr/]);
+            $self->cmd(qq[mkdir -p '$$self{known_hapref}/$chr/']);
             $self->cmd(qq[$CMD $knowns -merge_ref_panels -o $rg_prefix -merge_ref_panels_output_ref $rg_prefix]);
 
             unlink("$rg_prefix.hap.samples.part");
@@ -746,7 +746,7 @@ sub save_config
     my $src = $$self{_config};
     my $dst = "$$self{outdir}/impute2.conf";
     if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
-    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
+    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
     open(my $fh,'>',$dst) or $self->throw("$dst: $!");
     my $about = $$self{_about};
     $about =~ s/\n/\n# /g;
diff --git a/scripts/run-runners b/scripts/run-runners
index 5d1bcce..ed13c5d 100755
--- a/scripts/run-runners
+++ b/scripts/run-runners
@@ -79,9 +79,9 @@ sub parse_params
     $$opts{dropbox_conf} = "$$opts{dropbox}.conf";
 
     if ( !-d $$opts{dropbox_conf} ) { error("Incorrect dropbox prefix, the directory not found: $$opts{dropbox_conf}\n\n"); }
-    if ( !-e $$opts{dropbox_in} ) { `mkdir -p $$opts{dropbox_in}`; }
-    if ( !-e $$opts{dropbox_out} ) { `mkdir -p $$opts{dropbox_out}`; }
-    if ( !-e $$opts{dropbox_tmp} ) { `mkdir -p $$opts{dropbox_tmp}`; }
+    if ( !-e $$opts{dropbox_in} ) { `mkdir -p '$$opts{dropbox_in}'`; }
+    if ( !-e $$opts{dropbox_out} ) { `mkdir -p '$$opts{dropbox_out}'`; }
+    if ( !-e $$opts{dropbox_tmp} ) { `mkdir -p '$$opts{dropbox_tmp}'`; }
     if ( !exists($$opts{err_period}) ) { $$opts{err_period} = 60; }
 
     return $opts;
@@ -272,7 +272,7 @@ sub list_projects
         $project   = parse_project($opts,$$opts{dropbox_in},$name,$run_id);
         if ( !defined $project ) { next; }
 
-        system("mkdir -p $$opts{dropbox_tmp}/$$project{run_id}");
+        system("mkdir -p '$$opts{dropbox_tmp}/$$project{run_id}'");
         system("mv $$opts{dropbox_in}/$name $$opts{dropbox_tmp}/$$project{run_id}/$name");
         if ( $? ) { confess "mv $$opts{dropbox_in}/$name $$opts{dropbox_tmp}/$$project{run_id}/$name"; }
 
@@ -296,7 +296,7 @@ sub clean_project
         if ( ref($$project{outputs}{$outdir}) eq 'ARRAY' )
         {
             # create a subdirectory '$outdir' and copy all listed files in there
-            cmd($opts,"mkdir -p $$opts{dropbox_out}/$$project{run_id}/$outdir");
+            cmd($opts,"mkdir -p '$$opts{dropbox_out}/$$project{run_id}/$outdir'");
             for my $file (@{$$project{outputs}{$outdir}})
             {
                 my $path = expand_vars($opts,$project,$file);
@@ -312,13 +312,13 @@ sub clean_project
                 $dst = $$project{outputs}{$outdir};
                 if ( $dst =~ m{([^/]+)$} ) { $dir = "$dir/$`"; $dst = "$dir/$1"; }
             }
-            cmd($opts,"mkdir -p $dir");
+            cmd($opts,"mkdir -p '$dir'");
             my $path = expand_vars($opts,$project,$outdir);
             cmd($opts,"mv $path $dst");
         }
     }
 
-    cmd($opts,"mkdir -p $$opts{dropbox_out}/$$project{run_id}/tmp-data");
+    cmd($opts,"mkdir -p '$$opts{dropbox_out}/$$project{run_id}/tmp-data'");
     cmd($opts,"mv $$opts{dropbox_tmp}/$$project{run_id} $$opts{dropbox_out}/$$project{run_id}/tmp-data");
 }
 
@@ -535,7 +535,7 @@ sub run_project
             debug_msg($opts, "step done: $prefix.$step\n");
             next; 
         }
-        if ( ! -e $prefix ) { system("mkdir -p $prefix.$step"); }
+        if ( ! -e $prefix ) { system("mkdir -p '$prefix.$step'"); }
         $$project{step} = $step;
 
         if ( exists($$project{$step}{config}) && !-e "$prefix.$step.conf" )
diff --git a/scripts/run-shapeit b/scripts/run-shapeit
index f8f2900..9d9565e 100755
--- a/scripts/run-shapeit
+++ b/scripts/run-shapeit
@@ -229,7 +229,7 @@ sub mrProper
 sub runtime_stats
 {
     my ($self,$outfile) = @_;
-    $self->cmd("mkdir -p $outfile.part");
+    $self->cmd("mkdir -p '$outfile.part'");
     $self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
     rename("$outfile.part",$outfile) or $self->throw("rename $outfile.part $outfile: $!");
 }
@@ -468,7 +468,7 @@ sub ref_to_shapeit
     my $outdir = $outfile;
     $outdir =~ s{/[^/]*$}{};
     my $ref_vcf = $self->expand_chrom($$self{ref_vcf},$chr);
-    $self->cmd(qq[mkdir -p $outdir]);
+    $self->cmd(qq[mkdir -p '$outdir']);
     $self->cmd(qq[$$self{bcftools} convert -r $chr:$from-$to $ref_vcf --haplegendsample $outfile.part]);
     rename("$outfile.part.samples","${prefix}_samples") or $self->throw("rename $outfile.part.samples ${prefix}_samples: $!");
     rename("$outfile.part.legend.gz","${prefix}_legend.gz") or $self->throw("rename $outfile.part.legend.gz ${prefix}_legend.gz: $!");
@@ -543,7 +543,7 @@ sub vcf_to_shapeit
     my $to   = $$chunk[2];
     my $outdir = "$$self{outdir}/$chr";
     my $in_vcf = $self->expand_chrom($$self{in_vcf},$chr);
-    $self->cmd(qq[mkdir -p $outdir]);
+    $self->cmd(qq[mkdir -p '$outdir']);
     $self->cmd(qq[$$self{bcftools} view -r $chr:$from-$to -g ^miss -Ou $in_vcf | $$self{bcftools} convert --gensample $outdir/01.vcf_to_shapeit.$from-$to]);
     if ( exists($$self{fams}) ) { $self->set_families("$outdir/01.vcf_to_shapeit.$from-$to.samples"); }
     $self->cmd(qq[touch $outfile]);
@@ -640,7 +640,7 @@ sub save_config
     my $src = $$self{_config};
     my $dst = "$$self{outdir}/shapeit.conf";
     if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
-    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
+    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
     open(my $fh,'>',$dst) or $self->throw("$dst: $!");
     my $about = $$self{_about};
     $about =~ s/\n/\n# /g;
diff --git a/scripts/run-st-mpileup b/scripts/run-st-mpileup
index 58144e9..8a97734 100755
--- a/scripts/run-st-mpileup
+++ b/scripts/run-st-mpileup
@@ -381,7 +381,7 @@ sub clean
 sub runtime_stats
 {
     my ($self,$outfile) = @_;
-    $self->cmd("mkdir -p $outfile.part");
+    $self->cmd("mkdir -p '$outfile.part'");
     $self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
     open(my $fh,'>',"$outfile.part/info.txt") or $self->throw("$outfile.part/info.txt: $!");
     print $fh $$self{_about};
@@ -395,7 +395,7 @@ sub save_config
     my $src = $$self{_config};
     my $dst = "$$self{outdir}/mpileup.conf";
     if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
-    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
+    if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
     open(my $fh,'>',$dst) or $self->throw("$dst: $!");
     my $about = $$self{_about};
     $about =~ s/\n/\n# /g;
@@ -430,14 +430,14 @@ sub check_sanity
     {
         if ( !exists($bam_pls{$pl}) ) { $self->throw("The platform \"$pl\" not present in any of the BAMs.\n"); }
     }
-    `mkdir -p $$self{outdir}`;
+    `mkdir -p '$$self{outdir}'`;
     $self->cmd("touch $$self{outdir}/sanity_checked");
 }
 
 sub open_file
 {
     my ($self,$file) = @_;
-    if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p $1"); }
+    if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p '$1'"); }
     open(my $fh,'>',$file) or $self->throw("$file: $!");
     return $fh;
 }
@@ -819,7 +819,7 @@ sub all_site_bcfs
     my $outdir = $$self{outdir};
     my $bam_list = "$outdir/lists/chr$chr-$pop.list";
 
-    `mkdir -p $outdir/$pop/$chr/` unless -d "$outdir/$pop/$chr";
+    `mkdir -p '$outdir/$pop/$chr/'` unless -d "$outdir/$pop/$chr";
     my $cmd = "$$self{mpileup} -g -r $chr:$from-$to -b $bam_list -f $$self{fa_ref} > $outfile.part";
     $self->cmd($cmd);
 
@@ -837,7 +837,7 @@ sub call_variants
 
     $self->set_chunk_options($chr,$from,$to);
 
-    `mkdir -p $outdir/$pop/$chr/` unless -d "$outdir/$pop/$chr";
+    `mkdir -p '$outdir/$pop/$chr/'` unless -d "$outdir/$pop/$chr";
 
     # Create sample list with correct ploidy info
     my $sample_list = "$outdir/$pop/$chr/$chr:$from-$to.samples";