diff --git a/MinION_mobile_lab.R b/MinION_mobile_lab.R
index ee9bfa6..a79f3ec 100644
--- a/MinION_mobile_lab.R
+++ b/MinION_mobile_lab.R
@@ -222,6 +222,7 @@ if (pair_strands_flag == 1) {
   system(paste0(PYCOQC, " -f ", d2_basecalling, "/sequencing_summary.txt -b ", d2_preprocessing, "/barcoding_summary.txt -o ", d2, "/qc/pycoQC_report.html"))
 }
 demu_files <- list.files(path = d2_preprocessing, pattern = "BC", full.names = TRUE)
+
 for (i in 1:length(demu_files)) {
   BC_val_curr <- substr(x = basename(demu_files[i]), start = 3, stop = 4)
   if (paste0("BC", BC_val_curr) %in% BC_int) {
@@ -229,7 +230,7 @@ for (i in 1:length(demu_files)) {
     cat(text = paste0("Now trimming adapters with Porechop for sample BC", BC_val_curr), sep = "\n")
     if (disable_porechop_demu_flag == 1) {
       system(paste0("mkdir ", d2_preprocessing, "/BC", BC_val_curr, "_porechop_dir_tmp"))
-      system(paste0(PORECHOP, " -i ", d2_preprocessing, "/BC", BC_val_curr, "_tmp1.fastq -o ", d2_preprocessing, "/BC", BC_val_curr, "_porechop_dir_tmp/BC", BC_val_curr, ".fastq"))
+      system(paste0(PORECHOP, " -i ", d2_preprocessing, "/BC", BC_val_curr, "_tmp1.fastq -o ", d2_preprocessing, "/BC", BC_val_curr, "_porechop_dir_tmp/BC", BC_val_curr, ".fastq  --extra_end_trim ", primers_length))
     } else {
       system(paste0(PORECHOP, " -i ", d2_preprocessing, "/BC", BC_val_curr, "_tmp1.fastq -b ", d2_preprocessing, "/BC", BC_val_curr, "_porechop_dir_tmp --require_two_barcodes"))
     }
@@ -267,7 +268,7 @@ for (i in 1:length(demu_files)) {
       system(paste0("rm ", d3, "/BC", BC_val_curr, ".fastq"))
       system(paste0("rm ", d3, "/BC", BC_val_curr, ".fasta"))
       next
-    }
+    } 
     cat(text = paste0("Mean read length for sample BC", BC_val_curr, " after filtering: ", sprintf("%.0f", mean(ws_ok)), " (", sprintf("%.0f", sd(ws_ok)), ")"), file = logfile, sep = "\n", append = TRUE)
     cat(text = paste0("Mean read length for sample BC", BC_val_curr, " after filtering: ", sprintf("%.0f", mean(ws_ok)), " (", sprintf("%.0f", sd(ws_ok)), ")"), sep = "\n")
     png(paste0(d2, "/qc/hist_BC", BC_val_curr, "_unfiltered.png"))
diff --git a/config_MinION_mobile_lab.R b/config_MinION_mobile_lab.R
index 33c53de..300b5f5 100644
--- a/config_MinION_mobile_lab.R
+++ b/config_MinION_mobile_lab.R
@@ -21,7 +21,7 @@
 #if do_subsampling_flag <- 1, subsampling of num_fast5_files fast5 files is performed; otherwise set do_subsampling_flag <- 0
 do_subsampling_flag <- 0
 #num_fast5_files is the number of fast5 files to be subsampled/analysed (if do_subsampling_flag <- 1)                          
-num_fast5_files <- 25
+num_fast5_files <- 50000
 #BC_int are the barcodes used in the experiment
 #BC_int <- c("BC01", "BC02", "BC03", "BC04", "BC05", "BC06", "BC07", "BC08", "BC09", "BC10", "BC11", "BC12")
 BC_int <- c("BC01", "BC02", "BC03", "BC04", "BC05", "BC06", "BC07", "BC08", "BC09", "BC10", "BC11", "BC12")
@@ -41,8 +41,8 @@ save_space_flag <- 0
 #set the maximum number of threads to be used
 num_threads <- 30
 #set a mean amplicon length [bp]
-amplicon_length <- 700
-#fixed_lenfil_flag <- 1 if you want to keep reads in the range [amplicon_length - lenfil_tol/2; amplicon_length + lenfil_tol/2]; otherwise set fixed_lenfil_flag <- 0 if you want to keep reads in the range [mean_length -2*sd; mean_length + 2*sd] where mean_length and sd are evaluated on a sample basis
+amplicon_length <- 710
+#fixed_lenfil_flag <- 1 if you want to keep reads in the range [amplicon_length - lenfil_tol/2; amplicon_length + lenfil_tol/2]; otherwise set fixed_lenfil_flag <- 1 if you want to keep reads in the range [mean_length -2*sd; mean_length + 2*sd] where mean_length and sd are evaluated on a sample basis
 fixed_lenfil_flag <- 0
 #if fixed_lenfil_flag <- 1, lenfil_tol [bp] is the size of the window centered in amplicon_length for reads to be kept
 lenfil_tol <- 300
diff --git a/install.sh b/install.sh
index 16459b6..8f37bcf 100644
--- a/install.sh
+++ b/install.sh
@@ -19,12 +19,11 @@
 #
 
 PIPELINE_DIR=$(realpath $( dirname "${BASH_SOURCE[0]}" ))
-MINICONDA_DIR=$(which conda | sed 's/miniconda3.*$/miniconda3/')
+MINICONDA_DIR=$(which conda | sed 's/bin.*$//')
 conda config --add channels bioconda
 conda config --add channels conda-forge
 conda config --add channels r
-conda config --add channels anaconda
-conda create -n ONTrack_env python=3.6 blast emboss vsearch seqtk mafft porechop minimap2 samtools nanopolish bedtools r bioconductor-biostrings 
+conda create -n ONTrack_env python=3.6 blast emboss vsearch seqtk mafft porechop minimap2 samtools nanopolish r bioconductor-biostrings 
 source activate ONTrack_env
 pip install pycoQC
 echo -e "\n"
diff --git a/version.txt b/version.txt
index 25f1bf7..d88857a 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-ONTrack-v1.4.2
+ONTrack-v1.5.0