diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp
index 8f1f46c6e8cd2183495d006e4439df34a61bf97f..ee2dd575f517a65d1b3f1c4e045ca0220dbd9929 100644
--- a/src/ROCKparams.cpp
+++ b/src/ROCKparams.cpp
@@ -62,7 +62,6 @@ void ROCKparams::optArgConsistency(const string& input_file,const string& output
         usage(EXIT_FAILURE);
     }
     if (nb_k_mers) { // user indicated number of k-mers; use it to minimize parms.lambda
-        //parms.lambda=getBestLambdaForN(nb_k_mers,parms.lambda);
     	int smallest_kappa;
     	if (parms.kappa_prime==0) smallest_kappa=parms.kappa;
     	else smallest_kappa=parms.kappa_prime;
@@ -259,16 +258,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
     std::vector<string> v_input_lines;
     std::vector<string> v_output_lines;
     static int PE_separately=1;
-/*
-    static struct option long_options[] =
-    {
-        {"separate_PE", no_argument, &PE_as_single,0},
-        {0,0,0,0}
-    };*/
-
-    //int option_index=0;
 
-    // while((i = getopt_long(argc, argv, "i:o:l:k:c:C:g:n:vq:m:",long_options,&option_index)) != -1) {
     while((i = getopt(argc, argv, "i:o:l:k:c:C:n:vq:m:")) != -1) {
         switch(i) {
             case 0:
@@ -304,24 +294,9 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
                 break;
             case 'n':
                 nb_k_mers=atoi(optarg);break; // number of distinct k-mers
-/*            case 'g':
-                // cout<<optarg<<endl;
-                g=atoi(optarg);
-                break;*/
             case 'v':
                 verbose_mode=1;
                 break;
-/*            case 'p':
-                if (strlen(optarg)>1) {
-                    cout<<"value for -p option must be 0, 1 or 2";
-                    usage(EXIT_FAILURE);
-                }
-                PE_separately=atoi(optarg);
-                if (PE_separately<0 or PE_separately>2) {
-                    cout<<"value for -p option must be 0, 1 or 2";
-                    usage(EXIT_FAILURE);
-                }
-                break;*/
             case 'q':
                 q=atoi(optarg);
                 if (q<0) {
@@ -342,12 +317,6 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
             default:
                 usage(EXIT_FAILURE); break; }
     }
-    /*if (!PE_as_single && qual_thres.min_correct_k_mers_in_read!=1) {
-        cout<<"Incompatible options: when PE are processed independently, minimum number of correct k-mers in each end is 1."<<endl;
-        usage(EXIT_FAILURE);
-    }*/
-    //parms.filter_PE_separately=PE_separately;
-    //cout<<PE_as_single<<endl;
     processMainArgs(optind, argc, argv,v_input_lines);
     optArgConsistency(input_file,output_file,g,parms,nb_k_mers,v_input_lines);
     if (nb_k_mers) {
diff --git a/src/ROCKparams.h b/src/ROCKparams.h
index cfc0baa2288f3e88c2480eb3a8494971bd991e0b..96652c4043587387a0f0791e83c71fdfba023b15 100644
--- a/src/ROCKparams.h
+++ b/src/ROCKparams.h
@@ -87,7 +87,7 @@ public:
     ROCKparams() {
         f_id=0; // to generate id of input/output fastq files. +1=total number of files.
         g=0;
-        k=30;
+        k=25;
         nb_k_mers=0;
         parms.kappa=70;
         parms.kappa_prime=5;
diff --git a/src/main_utils.cpp b/src/main_utils.cpp
index 58ac7c5c025995e5553cc82a4ad31bc6e5a39023..3ec1bad524ff84f7fdbf8e9b9643ce8934b09dd9 100644
--- a/src/main_utils.cpp
+++ b/src/main_utils.cpp
@@ -69,7 +69,7 @@ std::string checkDirExists(const string o_file) {
  * logarithm of the gamma function;
  * from here: https://www.cec.uchile.cl/cinetica/pcordero/MC_libros/NumericalRecipesinC.pdf
  */
-//#include <stdio.h>
+
 double gammln(const unsigned long& xx) {
 	double x,y,tmp,ser;
 
@@ -134,17 +134,6 @@ int getBestLambdaForN(const unsigned long& nb_k_mers,const int& smallest_kappa,c
 	return min_l;
 }
 
-/*
-int getBestLambdaForN_altn(const unsigned long& nb_k_mers,const int& smallest_kappa,const unsigned int& m,const float& max_collision_proba) {
-    float ccdfr=ccdf(smallest_kappa,nb_k_mers,m);
-    int l=0;
-    float p=ccdfr;
-    while(l<50 and p>max_collision_proba) {
-        p*=ccdfr;
-        l++;
-    }
-    return l-1;
-}*/
 
 
 
@@ -159,13 +148,11 @@ void usage(int status) {
   cout<<"    -i <file>      .... file name containing the list of the FASTQ files to process."<<endl;
   cout<<"    -o <file>      .... file name containing the list of the output FASTQ file names."<<endl;
   cout<<"    -h             .... Print this message and exit."<<endl;
-  cout<<"    -k <int>       .... k-mer size. (default 30)."<<endl;
+  cout<<"    -k <int>       .... k-mer size. (default 25)."<<endl;
   cout<<"    -c <int>       .... lower coverage threshold (default: 5)."<<endl;
   cout<<"    -C <int>       .... upper coverage threshold (default: 70; max: 65535)."<<endl;
   cout<<"    -l <int>       .... size of the count min sketch (default: at most 4, depending on the available RAM)"<<endl;
   cout<<"    -n <int>       .... (expected) number of distinct k-mers within the processed reads."<<endl;
-  // cout<<"    -g <int>       .... maximum RAM to use (in Gb) for the CMS."<<endl;
-  // cout<<"    -p <int>       .... treat PE as single, separately with strict -c filter, separately with lenient -c fileter. Default is 1."<<endl;
   cout<<"    -q <int>       .... minimum quality threshold for nucleotides. Default is 10."<<endl;
   cout<<"    -m <int>       .... minimum of valid k-mer threshold for reads. Default is 1."<<endl;
   cout<<"    -v             .... verbose"<<endl;
diff --git a/src/main_utils.h b/src/main_utils.h
index d4458a9fbf41ed49f39abd66dc6f2227cfce699f..59e72e2d9c42d91a133f0917f88b5651579076e9 100644
--- a/src/main_utils.h
+++ b/src/main_utils.h
@@ -8,10 +8,6 @@
 #ifndef MAIN_UTILS_H_
 #define MAIN_UTILS_H_
 
-//#define k_max_input_files 15
-/*#define k_sep_pair_end ','
-#define k_ext '.'
-#define path_sep '/'*/
 
 #define k_max_collision_proba 0.1
 
diff --git a/test/rock_mem.sh b/test/rock_mem.sh
index 6b436a60d39ec83372323388a2c26bbd0b4b225a..eaed30fcf2cab5112b75eb558e8509604b7d6a4c 100755
--- a/test/rock_mem.sh
+++ b/test/rock_mem.sh
@@ -108,18 +108,18 @@ expected_diff2="> @SRR1222430.37 37 length=251 \
 > A3>333BFA2FF4GBFFDGGCGED?FGEGGHGFFFEEG?AF13@50>///11B13@@1/>//B0?>////<//B/00??@/--:--.;:C000;:0/0009.-9:.00:-.;9/9...-;.--9@--9:////-9-9..////9/;//;9///.9-..--------..99.9.//////;-;--9-.////://9/9.;.-;-99-.//.;////-;?9;...9-9-----9;-.;.;/.-9.;/99=--;"
 
 mkdir tmp
-../src/rock -C 100 -c 1 -l 2  -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 140
+../src/rock -C 100 -k 30 -c 1 -l 2  -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 140
 
-../src/rock -C 100 -c 1 -l 2 -q 2 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 141
+../src/rock -C 100 -k 30 -c 1 -l 2 -q 2 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 141
 
 ret1=`diff tmp/klebsiella_100_1_very_low_qual_thres.fq tmp/klebsiella_100_1_no_qual_thres.fq|wc -l`
 test $ret1 -eq 0 || exit 142
 ret2=`diff tmp/klebsiella_100_2_very_low_qual_thres.fq tmp/klebsiella_100_2_no_qual_thres.fq|wc -l`
 test $ret2 -eq 0 || exit 143
 
-../src/rock -C 100 -c 1 -l 2 -q 12 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_12.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 144
+../src/rock -C 100 -k 30 -c 1 -l 2 -q 12 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_12.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 144
 
-../src/rock -C 100 -c 1 -l 2 -q 13 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 145
+../src/rock -C 100 -k 30 -c 1 -l 2 -q 13 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 145
 
 ret1=`diff tmp/klebsiella_100_1_13_qual_thres.fq tmp/klebsiella_100_1_12_qual_thres.fq|grep -c "@SRR1222430.37"`
 test $ret1 -eq  1 || exit 146
@@ -140,9 +140,9 @@ echo "##########################################################################
 echo "testing ROCK with a quality score threshold for nucleotides and minimum number of valid k-mer to keep a read."
 
 mkdir tmp
-../src/rock -C 100 -c 1 -l 2 -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 150
+../src/rock -C 100 -k 30 -c 1 -l 2 -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 150
 
-../src/rock -C 100 -c 1 -l 2 -q 2 -m 5 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 151
+../src/rock -C 100 -k 30 -c 1 -l 2 -q 2 -m 5 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 151
 
 ret1=`diff tmp/klebsiella_100_1_very_low_qual_thres.fq tmp/klebsiella_100_1_no_qual_thres.fq|wc -l`
 test $ret1 -eq 0 || exit 152
@@ -159,7 +159,7 @@ ret2=`cat tmp/klebsiella_100_2.undefined.fq|wc -l`
 test $ret1 -eq 0 || exit 156
 test $ret1 -eq 0 || exit 157
 
-../src/rock -C 100 -c 1 -l 2 -q 13 -m 500 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 158
+../src/rock -k 30 -C 100 -c 1 -l 2 -q 13 -m 500 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 158
 
 [ -f "tmp/klebsiella_100_1.undefined.fq" ] || exit 159
 [ -f "tmp/klebsiella_100_2.undefined.fq" ] || exit 160
@@ -170,7 +170,7 @@ ret2=`cat tmp/klebsiella_100_2.undefined.fq|wc -l`
 test $ret1 -eq 400 || exit 161
 test $ret1 -eq 400 || exit 162
 
-../src/rock -C 100 -c 1 -l 2 -q 13 -m 300 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 163
+../src/rock -k 30 -C 100 -c 1 -l 2 -q 13 -m 300 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 163
 
 [ -f "tmp/klebsiella_100_1.undefined.fq" ] || exit 164
 [ -f "tmp/klebsiella_100_2.undefined.fq" ] || exit 165