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ManuelTgnManuelTgn
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Merge pull request #61 from pinellolab/test-error-tracing-grep
Test error tracing grep
2 parents 5d4ab25 + d3e7fe7 commit 21880c6

11 files changed

Lines changed: 595 additions & 561 deletions

‎PostProcess/extraction.sh‎

Lines changed: 8 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,7 @@
11
#!/bin/bash
22

3-
43
##NOTE AWK & GREP REPORT NO STDOUT IF NO MATCHES ARE FOUND (AWK DO NOT PRODUCE ANY OUTPUT)
5-
set -e # trace all errors
4+
# set -e # trace all errors
65

76
#PARAM $1 is ref targets file
87
#PARAM $2 is var targets file
@@ -12,40 +11,21 @@ dir=$(dirname $1)
1211
#common targets extraction
1312
LC_ALL=C sort -u -T "$dir" $1 >$1.sort.txt
1413
LC_ALL=C sort -u -T "$dir" $2 >$2.sort.txt
15-
cp $2.sort.txt $3.common_targets.txt
16-
# LC_ALL=C comm -12 $1.sort.txt $2.sort.txt >$3.common_targets.txt
14+
# cp $2.sort.txt $3.common_targets.txt
15+
LC_ALL=C comm -12 $1.sort.txt $2.sort.txt >$3.common_targets.txt
1716

1817
#Semi common targets extraction
19-
touch $3.ref.chr_pos.txt
20-
# LC_ALL=C awk '{print $4"\t"$5"\t"$6}' $1.sort.txt >$3.ref.chr_pos.txt
21-
# 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
22-
cp $2.sort.txt $3.semi_common_targets.txt
18+
LC_ALL=C awk '{print $4"\t"$5"\t"$6}' $1.sort.txt >$3.ref.chr_pos.txt
19+
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
2320

2421
#Aggiungo i target del ref: ora semicommon contiene: target con iupac e targets senza iupac corrispondenti;
2522
# target senza iupac del var e corrispondenti target senza iupac del ref
26-
# LC_ALL=C grep -F -f $3.ref.chr_pos.txt $1.sort.txt >>$3.semi_common_targets.txt
27-
# LC_ALL=C sort -u -T "$dir" $3.semi_common_targets.txt >$3.semi_common_targets.sort.txt
28-
cp $3.semi_common_targets.txt $3.semi_common_targets.sort.txt
23+
LC_ALL=C awk 'NR==FNR{a[$0]; next} ($4"\t"$5"\t"$6) in a' $3.ref.chr_pos.txt $1.sort.txt >>$3.semi_common_targets.txt
24+
LC_ALL=C sort -u -T "$dir" $3.semi_common_targets.txt >$3.semi_common_targets.sort.txt
2925

3026
#unique variant targets extraction
31-
# LC_ALL=C comm -13 $3.semi_common_targets.sort.txt $2.sort.txt >$3.unique_targets.txt
32-
cp $2.sort.txt $3.unique_targets.txt
27+
LC_ALL=C comm -13 $3.semi_common_targets.sort.txt $2.sort.txt >$3.unique_targets.txt
3328

3429
mv $3.semi_common_targets.sort.txt $3.semi_common_targets.txt
3530
#Remove tmp files, NOTE maybe keep first two and change name to $1 and $2 ?
3631
rm $1.sort.txt $2.sort.txt $3.ref.chr_pos.txt
37-
38-
# # OLD semi common targets extraction
39-
# LC_ALL=C awk '{print $4"\t"$5}' $1 > ref.chr_pos.txt
40-
# LC_ALL=C sort -T ./ -u ref.chr_pos.txt > ref.chr_pos.sort.txt
41-
# LC_ALL=C grep -F -f ref.chr_pos.sort.txt $2 > $3.semi_common_targets.txt
42-
# LC_ALL=C awk '{print $4"\t"$5}' $3.semi_common_targets.txt > semi_common.chr_pos.txt
43-
# LC_ALL=C sort -T ./ -u semi_common.chr_pos.txt > semi_common.chr_pos.sort.txt
44-
# LC_ALL=C grep -F -f semi_common.chr_pos.sort.txt $1 >> $3.semi_common_targets.txt
45-
# LC_ALL=C sort -T ./ -u $3.semi_common_targets.txt > semi_common_targets.sort.txt
46-
47-
# # OLD unique variant targets extraction
48-
# #LC_ALL=C sort $2 > $2.sort.txt
49-
# LC_ALL=C comm -13 semi_common_targets.sort.txt $2.sort.txt > $3.unique_targets.txt
50-
51-
# 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

‎PostProcess/merge_alt_chr.sh‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,25 +1,24 @@
11
#!/bin/bash
22

3-
set -e # trace all failures
3+
set -e # trace all failures
44

55
dir=$(dirname $1)
66
fileIn=$1
77
fileOut=$2
88

99
STARTTIME=$(date +%s)
1010

11-
chroms=($(cut -f 5 $fileIn | tail -n +2 | LC_ALL=C grep -v "_" | LC_ALL=C sort -T "$dir" | uniq))
11+
chroms=($(awk 'NR>1 && !/_/ {print $5}' $fileIn | LC_ALL=C sort -T "$dir" | uniq))
1212

1313
head -1 $fileIn >$fileOut
1414

1515
for chrom in ${chroms[@]}; do
1616

1717
echo $chrom
18-
#awk -v "key=$chrom" '$5 == key {print($0)}' $fileIn > $fileIn.$chrom.ref
19-
grep -F -w "$chrom" $fileIn >$fileIn.$chrom.ref
18+
awk "/${chrom}\t/" test.targets.txt >$fileIn.$chrom.ref
2019
cut -f 3 $fileIn.$chrom.ref | LC_ALL=C sort -T "$dir" | uniq >$fileIn.$chrom.ref.targets
21-
LC_ALL=C grep -F "${chrom}_" $fileIn >$fileIn.$chrom.alt # | awk '$5 ~ "_" {print($0)}'
22-
LC_ALL=C grep -v -F -f $fileIn.$chrom.ref.targets $fileIn.$chrom.alt >$fileIn.$chrom.merged
20+
awk -v chrom="$chrom" '$0 ~ chrom"_" {print($0)}' $fileIn >$fileIn.$chrom.alt
21+
awk 'NR==FNR{a[$0];next} !($0 in a)' $fileIn.$chrom.ref.targets $fileIn.$chrom.alt >$fileIn.$chrom.merged
2322
rm $fileIn.$chrom.ref.targets
2423
rm $fileIn.$chrom.alt
2524
cat $fileIn.$chrom.ref $fileIn.$chrom.merged >>$fileOut

‎PostProcess/merge_close_targets_cfd.sh‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/bin/bash
22

3-
set -e # capture any failure
3+
# set -e # capture any failure
44

55
fileIn=$1
66
fileOut=$2
@@ -28,8 +28,9 @@ echo "Sorting done in $(($ENDTIME - $STARTTIME)) seconds"
2828
# rm $fileIn.sorted.tmp
2929
echo "Merging contiguous targets"
3030
# python remove_contiguous_samples_cfd.py $fileIn.sorted $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd
31-
python remove_contiguous_samples_cfd.py $fileIn $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd $sort_pivot $sorting_criteria_scoring $sorting_criteria || {
32-
echo "CRISPRme ERROR: contigous SNP removal failed (script: ${0} line $((LINENO-1)))" >&2
33-
exit 1
34-
}
31+
python remove_contiguous_samples_cfd.py $fileIn $fileOut $thresh $chrom $position $total $true_guide $snp_info $cfd $sort_pivot $sorting_criteria_scoring $sorting_criteria
32+
# 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 || {
33+
# echo "CRISPRme ERROR: contigous SNP removal failed (script: ${0} line $((LINENO-1)))" >&2
34+
# exit 1
35+
# }
3536
# rm $fileIn.sorted

‎PostProcess/post_analisi_indel.sh‎

Lines changed: 45 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,13 @@
11
#!/bin/bash
22

3-
set -e
3+
# set -e
4+
5+
output_folder=$1
6+
ref_folder=$2
7+
ref_name=$(basename $2)
8+
vcf_folder=$3 #!/bin/bash
9+
10+
set -e
411

512
output_folder=$1
613
ref_folder=$2
@@ -28,22 +35,49 @@ echo "Processing INDELs results for $key, starting post-analysis"
2835
true_chr=$key
2936
fake_chr="fake$true_chr"
3037

31-
# 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"
38+
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"
39+
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"
40+
header=$(head -1 $output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt)
41+
sed -i 1i"$header" "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
42+
43+
./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" || {
44+
echo "CRISPRme ERROR: indels analysis failed (script: ${0} line $((LINENO - 1)))" >&2
45+
exit 1
46+
}
47+
rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
48+
rm "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
49+
50+
vcf_name=$(basename $3)
51+
guide_file=$4
52+
guide_name=$(basename $4)
53+
mm=$5
54+
bDNA=$6
55+
bRNA=$7
56+
annotation_file=$8
57+
annotation_name=$(basename $8)
58+
pam_file=$9
59+
pam_name=$(basename $9)
60+
# sampleID=${10}
61+
dict_folder=${10}
62+
63+
final_res=${11}
64+
final_res_alt=${12}
65+
66+
key=${13}
67+
68+
echo "Processing INDELs results for $key, starting post-analysis"
69+
true_chr=$key
70+
fake_chr="fake$true_chr"
71+
3272
# create file to prevent void grep failing
3373
touch "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
3474
# create file to prevent void grep failing
3575
touch "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
36-
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"
76+
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"
3777
header=$(head -1 $output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt)
3878
sed -i 1i"$header" "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
3979

4080
./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" || {
41-
echo "CRISPRme ERROR: indels analysis failed (script: ${0} line $((LINENO-1)))" >&2
42-
exit 1
81+
echo "CRISPRme ERROR: indels analysis failed (script: ${0} line $((LINENO - 1)))" >&2
82+
exit 1
4383
}
44-
# rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
45-
# rm "$output_folder/crispritz_targets/indels_${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$true_chr"
46-
# 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"
47-
# 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"
48-
# rm "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key.bestMerge.txt"
49-
# rm "$output_folder/${fake_chr}_${pam_name}_${guide_name}_${annotation_name}_${mm}_${bDNA}_${bRNA}_$key.altMerge.txt"

‎PostProcess/post_analisi_snp.sh‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/bin/bash
22

3-
set -e # trace all command failures
3+
set -e # trace all command failures
44

55
output_folder=$1
66
ref_folder=$2
@@ -23,16 +23,15 @@ final_res_alt=${12}
2323

2424
key=${13}
2525

26-
2726
echo "Processing SNPs for $key"
28-
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"
27+
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"
2928
if ! [ -f "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt" ]; then
3029
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"
3130
else
32-
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"
31+
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"
3332
fi
3433
./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" || {
35-
echo "CRISPRme ERROR: SNP analysis failed (script: ${0} line $((LINENO-1)))" >&2
34+
echo "CRISPRme ERROR: SNP analysis failed (script: ${0} line $((LINENO - 1)))" >&2
3635
exit 1
3736
}
3837
rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"

‎PostProcess/post_analysis_only.sh‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/bin/bash
22

3-
set -e # trace all failures
3+
set -e # trace all failures
44

55
#file for automated search of guide+pam in reference and variant genomes
66

@@ -122,7 +122,7 @@ if [ "$vcf_name" != "_" ]; then
122122
fi
123123

124124
./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 || {
125-
echo "CRISPRme ERROR: indels postprocessing failed (script: ${0} line $((LINENO-1)))" >&2
125+
echo "CRISPRme ERROR: indels postprocessing failed (script: ${0} line $((LINENO - 1)))" >&2
126126
exit 1
127127
}
128128

@@ -153,10 +153,10 @@ else
153153
fi
154154
for key in "${real_chroms[@]}"; do
155155
echo "Processing $key"
156-
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"
156+
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"
157157
touch "$output_folder/crispritz_targets/${ref_name}+${vcf_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
158158
./scriptAnalisiNNN_v3.sh "$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" || {
159-
echo "CRISPRme ERROR: analysis failed (script: ${0} line $((LINENO-1)))" >&2
159+
echo "CRISPRme ERROR: analysis failed (script: ${0} line $((LINENO - 1)))" >&2
160160
exit 1
161161
}
162162
rm "$output_folder/crispritz_targets/${ref_name}_${pam_name}_${guide_name}_${mm}_${bDNA}_${bRNA}.targets.txt.$key"
@@ -181,7 +181,7 @@ if [ "$vcf_name" != "_" ]; then
181181

182182
echo "Post-analysis INDELs Start: "$(date +%F-%T) >>$output_folder/$log
183183
./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 || {
184-
echo "CRISPRme ERROR:indels analysis failed (script: ${0} line $((LINENO-1)))" >&2
184+
echo "CRISPRme ERROR:indels analysis failed (script: ${0} line $((LINENO - 1)))" >&2
185185
exit 1
186186
}
187187
echo "Post-analysis INDELs End: "$(date +%F-%T) >>$output_folder/$log
@@ -198,7 +198,7 @@ cd "$starting_dir"
198198

199199
echo "Merging Close Targets Start: "$(date +%F-%T) >>$output_folder/$log
200200
./merge_close_targets_cfd.sh $final_res $final_res.trimmed $merge_t || {
201-
echo "CRISPRme ERROR: CFD targets merge failed (script: ${0} line $((LINENO-1)))" >&2
201+
echo "CRISPRme ERROR: CFD targets merge failed (script: ${0} line $((LINENO - 1)))" >&2
202202
exit 1
203203
}
204204
mv $final_res.trimmed $final_res
@@ -209,8 +209,8 @@ mv $final_res.trimmed.discarded_samples $final_res_alt
209209
echo "Merging Close Targets End: "$(date +%F-%T) >>$output_folder/$log
210210

211211
echo "Merging Alternative Chromosomes Start: "$(date +%F-%T) >>$output_folder/$log
212-
./merge_alt_chr.sh $final_res $final_res.chr_merged || {
213-
echo "CRISPRme ERROR: alternative targets merge failed (script: ${0} line $((LINENO-1)))" >&2
212+
./merge_alt_chr.sh $final_res $final_res.chr_merged || {
213+
echo "CRISPRme ERROR: alternative targets merge failed (script: ${0} line $((LINENO - 1)))" >&2
214214
exit 1
215215
}
216216
#rm $final_res.trimmed
@@ -231,7 +231,7 @@ if ! [ -d "$output_folder/cfd_graphs" ]; then
231231
mkdir $output_folder/cfd_graphs
232232
fi
233233
./assemble_cfd_graphs.py $output_folder || {
234-
echo "CRISPRme ERROR: CFD graph creation failed (script: ${0} line $((LINENO-1)))" >&2
234+
echo "CRISPRme ERROR: CFD graph creation failed (script: ${0} line $((LINENO - 1)))" >&2
235235
exit 1
236236
}
237237
mv $output_folder/snps.CFDGraph.txt $output_folder/cfd_graphs

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