Merge pull request #61 from pinellolab/test-error-tracing-grep

Test error tracing grep
pinellolab · Aug 7, 2024 · 21880c6 · 21880c6
2 parents 5d4ab25 + d3e7fe7
commit 21880c6
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diff --git a/PostProcess/extraction.sh b/PostProcess/extraction.sh
@@ -1,8 +1,7 @@
 #!/bin/bash
 
-
 ##NOTE AWK & GREP REPORT NO STDOUT IF NO MATCHES ARE FOUND (AWK DO NOT PRODUCE ANY OUTPUT)
-set -e  # trace all errors
+# set -e # trace all errors
 
 #PARAM $1 is ref targets file
 #PARAM $2 is var targets file
@@ -12,40 +11,21 @@ dir=$(dirname $1)
 #common targets extraction
 LC_ALL=C sort -u -T "$dir" $1 >$1.sort.txt
 LC_ALL=C sort -u -T "$dir" $2 >$2.sort.txt
-cp $2.sort.txt $3.common_targets.txt
-# LC_ALL=C comm -12 $1.sort.txt $2.sort.txt >$3.common_targets.txt
+# cp $2.sort.txt $3.common_targets.txt
+LC_ALL=C comm -12 $1.sort.txt $2.sort.txt >$3.common_targets.txt
 
 #Semi common targets extraction
-touch $3.ref.chr_pos.txt
-# LC_ALL=C awk '{print $4"\t"$5"\t"$6}' $1.sort.txt >$3.ref.chr_pos.txt
-# LC_ALL=C grep -F -f $3.ref.chr_pos.txt $2.sort.txt >$3.semi_common_targets.txt #Seleziono i targets di var che hanno la stessa chr pos in ref
-cp $2.sort.txt $3.semi_common_targets.txt
+LC_ALL=C awk '{print $4"\t"$5"\t"$6}' $1.sort.txt >$3.ref.chr_pos.txt
+LC_ALL=C awk 'NR==FNR{a[$0]; next} {if ($4"\t"$5"\t"$6 in a) print $0}' $3.ref.chr_pos.txt $2.sort.txt >$3.semi_common_targets.txt
 
 #Aggiungo i target del ref: ora semicommon contiene: target con iupac e targets senza iupac corrispondenti;
 # target senza iupac del var e corrispondenti target senza iupac del ref
-# LC_ALL=C grep -F -f $3.ref.chr_pos.txt $1.sort.txt >>$3.semi_common_targets.txt
-# LC_ALL=C sort -u -T "$dir" $3.semi_common_targets.txt >$3.semi_common_targets.sort.txt
-cp $3.semi_common_targets.txt $3.semi_common_targets.sort.txt
+LC_ALL=C awk 'NR==FNR{a[$0]; next} ($4"\t"$5"\t"$6) in a' $3.ref.chr_pos.txt $1.sort.txt >>$3.semi_common_targets.txt
+LC_ALL=C sort -u -T "$dir" $3.semi_common_targets.txt >$3.semi_common_targets.sort.txt
 
 #unique variant targets extraction
-# LC_ALL=C comm -13 $3.semi_common_targets.sort.txt $2.sort.txt >$3.unique_targets.txt
-cp $2.sort.txt $3.unique_targets.txt
+LC_ALL=C comm -13 $3.semi_common_targets.sort.txt $2.sort.txt >$3.unique_targets.txt
 
 mv $3.semi_common_targets.sort.txt $3.semi_common_targets.txt
 #Remove tmp files, NOTE maybe keep first two and change name to $1 and $2 ?
 rm $1.sort.txt $2.sort.txt $3.ref.chr_pos.txt
-
-# # OLD semi common targets extraction
-# LC_ALL=C awk '{print $4"\t"$5}' $1 > ref.chr_pos.txt
-# LC_ALL=C sort -T ./ -u ref.chr_pos.txt > ref.chr_pos.sort.txt
-# LC_ALL=C grep -F -f ref.chr_pos.sort.txt  $2 > $3.semi_common_targets.txt
-# LC_ALL=C awk '{print $4"\t"$5}' $3.semi_common_targets.txt > semi_common.chr_pos.txt
-# LC_ALL=C sort -T ./ -u semi_common.chr_pos.txt > semi_common.chr_pos.sort.txt
-# LC_ALL=C grep -F -f semi_common.chr_pos.sort.txt  $1 >> $3.semi_common_targets.txt
-# LC_ALL=C sort -T ./ -u $3.semi_common_targets.txt > semi_common_targets.sort.txt
-
-# # OLD unique variant targets extraction
-# #LC_ALL=C sort $2 > $2.sort.txt
-# LC_ALL=C comm -13 semi_common_targets.sort.txt $2.sort.txt > $3.unique_targets.txt
-
-# rm ref.chr_pos.txt ref.chr_pos.sort.txt semi_common_targets.sort.txt $2.sort.txt semi_common.chr_pos.txt semi_common.chr_pos.sort.txt $1.sort.txt
diff --git a/PostProcess/merge_alt_chr.sh b/PostProcess/merge_alt_chr.sh
@@ -1,25 +1,24 @@
 #!/bin/bash
 
-set -e  # trace all failures
+set -e # trace all failures
 
 dir=$(dirname $1)
 fileIn=$1
 fileOut=$2
 
 STARTTIME=$(date +%s)
 
-chroms=($(cut -f 5 $fileIn | tail -n +2 | LC_ALL=C grep -v "_" | LC_ALL=C sort -T "$dir" | uniq))
+chroms=($(awk 'NR>1 && !/_/ {print $5}' $fileIn | LC_ALL=C sort -T "$dir" | uniq))
 
 head -1 $fileIn >$fileOut
 
 for chrom in ${chroms[@]}; do
 
     echo $chrom
-    #awk -v "key=$chrom" '$5 == key {print($0)}' $fileIn > $fileIn.$chrom.ref
-    grep -F -w "$chrom" $fileIn >$fileIn.$chrom.ref
+    awk "/${chrom}\t/" test.targets.txt >$fileIn.$chrom.ref
     cut -f 3 $fileIn.$chrom.ref | LC_ALL=C sort -T "$dir" | uniq >$fileIn.$chrom.ref.targets
-    LC_ALL=C grep -F "${chrom}_" $fileIn >$fileIn.$chrom.alt # | awk '$5 ~ "_" {print($0)}'
-    LC_ALL=C grep -v -F -f $fileIn.$chrom.ref.targets $fileIn.$chrom.alt >$fileIn.$chrom.merged
+    awk -v chrom="$chrom" '$0 ~ chrom"_" {print($0)}' $fileIn >$fileIn.$chrom.alt
+    awk 'NR==FNR{a[$0];next} !($0 in a)' $fileIn.$chrom.ref.targets $fileIn.$chrom.alt >$fileIn.$chrom.merged
     rm $fileIn.$chrom.ref.targets
     rm $fileIn.$chrom.alt
     cat $fileIn.$chrom.ref $fileIn.$chrom.merged >>$fileOut

diff --git a/PostProcess/merge_close_targets_cfd.sh b/PostProcess/merge_close_targets_cfd.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e  # capture any failure
+# set -e  # capture any failure
 
 fileIn=$1
 fileOut=$2
@@ -28,8 +28,9 @@ echo "Sorting done in $(($ENDTIME - $STARTTIME)) seconds"
 # rm $fileIn.sorted.tmp
 echo "Merging contiguous targets"
 # python remove_contiguous_samples_cfd.py $fileIn.sorted $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd
-python remove_contiguous_samples_cfd.py $fileIn $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd $sort_pivot $sorting_criteria_scoring $sorting_criteria || {
-    echo "CRISPRme ERROR: contigous SNP removal failed (script: ${0} line $((LINENO-1)))" >&2
-	exit 1
-}
+python remove_contiguous_samples_cfd.py $fileIn $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd $sort_pivot $sorting_criteria_scoring $sorting_criteria
+# python remove_contiguous_samples_cfd_new.py $fileIn $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd $sort_pivot $sorting_criteria_scoring $sorting_criteria || {
+#     echo "CRISPRme ERROR: contigous SNP removal failed (script: ${0} line $((LINENO-1)))" >&2
+# 	exit 1
+# }
 # rm $fileIn.sorted
diff --git a/PostProcess/post_analisi_indel.sh b/PostProcess/post_analisi_indel.sh
@@ -1,6 +1,13 @@
 #!/bin/bash
 
-set -e 
+# set -e
+
+output_folder=$1
+ref_folder=$2
+ref_name=$(basename $2)
+vcf_folder=$3 #!/bin/bash
+
+set -e
 
 output_folder=$1
 ref_folder=$2
@@ -28,22 +35,49 @@ echo "Processing INDELs results for $key, starting post-analysis"
 true_chr=$key
 fake_chr="fake$true_chr"
 
-# LC_ALL=C grep -F -w $fake_chr "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+awk -v fake_chr="$fake_chr" '$0 ~ fake_chr {print}' "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+awk -v fake_chr="$fake_chr" '$0 ~ fake_chr {print}' "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+header=$(head -1 $output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt)
+sed -i 1i"$header" "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+
+./analisi_indels_NNN.sh "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr" "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr" "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}" "$annotation_file" "$dict_folder/log_indels_$vcf_name" "$ref_folder/$true_chr.fa" $mm $bDNA $bRNA "$guide_file" "$pam_file" "$output_folder" || {
+    echo "CRISPRme ERROR: indels analysis failed (script: ${0} line $((LINENO - 1)))" >&2
+    exit 1
+}
+rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+rm "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+
+vcf_name=$(basename $3)
+guide_file=$4
+guide_name=$(basename $4)
+mm=$5
+bDNA=$6
+bRNA=$7
+annotation_file=$8
+annotation_name=$(basename $8)
+pam_file=$9
+pam_name=$(basename $9)
+# sampleID=${10}
+dict_folder=${10}
+
+final_res=${11}
+final_res_alt=${12}
+
+key=${13}
+
+echo "Processing INDELs results for $key, starting post-analysis"
+true_chr=$key
+fake_chr="fake$true_chr"
+
 # create file to prevent void grep failing
 touch "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
 # create file to prevent void grep failing
 touch "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
-LC_ALL=C grep -F -w $fake_chr "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
+awk -v fake_chr="$fake_chr" '$0 ~ fake_chr {print}' "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
 header=$(head -1 $output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt)
 sed -i 1i"$header" "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
 
 ./analisi_indels_NNN.sh "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr" "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr" "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}" "$annotation_file" "$dict_folder/log_indels_$vcf_name" "$ref_folder/$true_chr.fa" $mm $bDNA $bRNA "$guide_file" "$pam_file" "$output_folder" || {
-    echo "CRISPRme ERROR: indels analysis failed (script: ${0} line $((LINENO-1)))" >&2
-	exit 1
+    echo "CRISPRme ERROR: indels analysis failed (script: ${0} line $((LINENO - 1)))" >&2
+    exit 1
 }
-# rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
-# rm "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
-# tail -n +2 "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key.bestMerge.txt" >> "$final_res" #"$output_folder/${fake_chr}_${guide_name}_${mm}_${bDNA}_${bRNA}.bestCFD.txt.tmp"
-# tail -n +2 "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key.altMerge.txt" >> "$final_res_alt" #"$output_folder/${fake_chr}_${guide_name}_${mm}_${bDNA}_${bRNA}.altCFD.txt.tmp"
-# rm "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key.bestMerge.txt"
-# rm "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key.altMerge.txt"
diff --git a/PostProcess/post_analisi_snp.sh b/PostProcess/post_analisi_snp.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e  # trace all command failures
+set -e # trace all command failures
 
 output_folder=$1
 ref_folder=$2
@@ -23,16 +23,15 @@ final_res_alt=${12}
 
 key=${13}
 
-
 echo "Processing SNPs for $key"
-LC_ALL=C grep -F -w $key "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
+awk -v key="$key" '{ if ($0 ~ key) print }' "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
 if ! [ -f "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" ]; then
 	cp "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key" "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
 else
-	LC_ALL=C grep -F -w $key "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
+	awk -v key="$key" '$0 ~ key' "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
 fi
 ./scriptAnalisiNNN_v3.sh "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.${key}" "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.${key}" "$output_folder/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key" "$annotation_file" "${dict_folder}/my_dict_${key}.json" "${ref_folder}/${key}.fa" $mm $bDNA $bRNA "$guide_file" "$pam_file" "$output_folder" || {
-	echo "CRISPRme ERROR: SNP analysis failed (script: ${0} line $((LINENO-1)))" >&2
+	echo "CRISPRme ERROR: SNP analysis failed (script: ${0} line $((LINENO - 1)))" >&2
 	exit 1
 }
 rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"

diff --git a/PostProcess/post_analysis_only.sh b/PostProcess/post_analysis_only.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e  # trace all failures
+set -e # trace all failures
 
 #file for automated search of guide+pam in reference and variant genomes
 
@@ -122,7 +122,7 @@ if [ "$vcf_name" != "_" ]; then
 	fi
 
 	./pool_post_analisi_snp.py $output_folder $ref_folder $vcf_name $guide_file $mm $bDNA $bRNA $annotation_file $pam_file $sampleID $dict_folder $final_res $final_res_alt $ncpus || {
-		echo "CRISPRme ERROR: indels postprocessing failed (script: ${0} line $((LINENO-1)))" >&2
+		echo "CRISPRme ERROR: indels postprocessing failed (script: ${0} line $((LINENO - 1)))" >&2
 		exit 1
 	}
 
@@ -153,10 +153,10 @@ else
 	fi
 	for key in "${real_chroms[@]}"; do
 		echo "Processing $key"
-		LC_ALL=C grep -F -w $key "$output_folder/crispritz_targets/${ref_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
+		awk -v key="$key" '$0 ~ key { print }' "$output_folder/crispritz_targets/${ref_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" >"$output_folder/crispritz_targets/${ref_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
 		touch "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
 		./scriptAnalisiNNN_v3.sh "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key" "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key" "${ref_name}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key" "$annotation_file" "_" "$ref_folder" $mm $bDNA $bRNA "$guide_file" "$pam_file" "$sampleID" "$output_folder" || {
-			echo "CRISPRme ERROR: analysis failed (script: ${0} line $((LINENO-1)))" >&2
+			echo "CRISPRme ERROR: analysis failed (script: ${0} line $((LINENO - 1)))" >&2
 			exit 1
 		}
 		rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
@@ -181,7 +181,7 @@ if [ "$vcf_name" != "_" ]; then
 
 	echo "Post-analysis INDELs Start: "$(date +%F-%T) >>$output_folder/$log
 	./pool_post_analisi_indel.py $output_folder $ref_folder $vcf_folder $guide_file $mm $bDNA $bRNA $annotation_file $pam_file $sampleID "$output_folder/log_indels_$vcf_name" $final_res $final_res_alt $ncpus || {
-		echo "CRISPRme ERROR:indels analysis failed (script: ${0} line $((LINENO-1)))" >&2
+		echo "CRISPRme ERROR:indels analysis failed (script: ${0} line $((LINENO - 1)))" >&2
 		exit 1
 	}
 	echo "Post-analysis INDELs End: "$(date +%F-%T) >>$output_folder/$log
@@ -198,7 +198,7 @@ cd "$starting_dir"
 
 echo "Merging Close Targets Start: "$(date +%F-%T) >>$output_folder/$log
 ./merge_close_targets_cfd.sh $final_res $final_res.trimmed $merge_t || {
-	echo "CRISPRme ERROR: CFD targets merge failed (script: ${0} line $((LINENO-1)))" >&2
+	echo "CRISPRme ERROR: CFD targets merge failed (script: ${0} line $((LINENO - 1)))" >&2
 	exit 1
 }
 mv $final_res.trimmed $final_res
@@ -209,8 +209,8 @@ mv $final_res.trimmed.discarded_samples $final_res_alt
 echo "Merging Close Targets End: "$(date +%F-%T) >>$output_folder/$log
 
 echo "Merging Alternative Chromosomes Start: "$(date +%F-%T) >>$output_folder/$log
-./merge_alt_chr.sh $final_res $final_res.chr_merged  || {
-	echo "CRISPRme ERROR: alternative targets merge failed (script: ${0} line $((LINENO-1)))" >&2
+./merge_alt_chr.sh $final_res $final_res.chr_merged || {
+	echo "CRISPRme ERROR: alternative targets merge failed (script: ${0} line $((LINENO - 1)))" >&2
 	exit 1
 }
 #rm $final_res.trimmed
@@ -231,7 +231,7 @@ if ! [ -d "$output_folder/cfd_graphs" ]; then
 	mkdir $output_folder/cfd_graphs
 fi
 ./assemble_cfd_graphs.py $output_folder || {
-	echo "CRISPRme ERROR: CFD graph creation failed (script: ${0} line $((LINENO-1)))" >&2
+	echo "CRISPRme ERROR: CFD graph creation failed (script: ${0} line $((LINENO - 1)))" >&2
 	exit 1
 }
 mv $output_folder/snps.CFDGraph.txt $output_folder/cfd_graphs