Fixed the subset of reads in aln

wgbs-pipeline.sh

@@ -29,8 +29,8 @@ meth_prop=$( realpath ./apps/methylation_proportion.py )
 
 # exit when any command fails
 set -e
-trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
-trap 'echo "\"${last_command}\" command filed with exit code $?"' EXIT
+#trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
+#trap 'echo "\"${last_command}\" command filed with exit code $?"' EXIT
 
 if [[ $# -lt 3 ]]; then
     echo "ERROR: Provide fastq files (R1 and R2) and the output folder!"
@@ -134,8 +134,8 @@ echo "##################################################"
 
  
 echo -ne "     1.1 Aligning... "
-#CMD="${bismark} ${b38_ref} -1 ${R1} -2 ${R2} --multicore 8 \
-CMD="${bismark} ${b38_ref} -1 ${R1} -2 ${R2} -u 10000 \
+#CMD="${bismark} ${b38_ref} -1 ${R1} -2 ${R2} -u 10000 \
+CMD="${bismark} ${b38_ref} -1 ${R1} -2 ${R2} --multicore 8 \
     -o ${output_dir} --prefix b38 --path_to_bowtie ${bowtie_path} \
     --samtools_path ${samtools_path} > ${log_dir}/1_1_aln.stdout 2> ${log_dir}/1_1_aln.stderr"
 echo -e ${CMD} > ${log_dir}/1_1_aln.cmd
@@ -259,8 +259,8 @@ echo "##################################################"
 
  
 echo -ne "     2.1 Aligning... "
-#CMD="${bismark} ${mt_ref} -1 ${R1} -2 ${R2} --multicore 8 \
-CMD="${bismark} ${mt_ref} -1 ${R1} -2 ${R2} -u 10000 \
+#CMD="${bismark} ${mt_ref} -1 ${R1} -2 ${R2} -u 10000 \
+CMD="${bismark} ${mt_ref} -1 ${R1} -2 ${R2} --multicore 8 \
     -o ${output_dir} --prefix MT --path_to_bowtie ${bowtie_path} \
     --samtools_path ${samtools_path} > ${log_dir}/2_1_aln.stdout 2> ${log_dir}/2_1_aln.stderr"
 echo -e ${CMD} > ${log_dir}/2_1_aln.cmd
@@ -359,8 +359,8 @@ echo "##################################################"
  
  
 echo -ne "     3.1 Aligning vs nuclear DNA... "
-#CMD="${bismark} ${nuc_ref} -1 ${R1} -2 ${R2} --multicore 8 \
-CMD="${bismark} ${nuc_ref} -1 ${R1} -2 ${R2} -u 10000 \
+#CMD="${bismark} ${nuc_ref} -1 ${R1} -2 ${R2} -u 10000 \
+CMD="${bismark} ${nuc_ref} -1 ${R1} -2 ${R2} --multicore 8 \
     --un --ambiguous -o ${output_dir} --prefix b38_noMT --path_to_bowtie ${bowtie_path} \
     --samtools_path ${samtools_path} > ${log_dir}/3_1_aln.stdout 2> ${log_dir}/3_1_aln.stderr"
 echo -e ${CMD} > ${log_dir}/3_1_aln.cmd