CRISPResso version 2.3.1
[Command used]:
/software/EasyBuild/Intel_Xeon_Platinum_8358_CPU__2.60GHz/software/crispresso2/2.3.1/bin/CRISPResso -o /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch --name Sample002 --exclude_bp_from_left 15 --needleman_wunsch_gap_open -20 --exclude_bp_from_right 15 --min_single_bp_quality 0 --conversion_nuc_to T --aln_seed_len 10 --min_paired_end_reads_overlap 10 --max_paired_end_reads_overlap None --needleman_wunsch_gap_extend -2 --quantification_window_size 1 --n_processes 6 --needleman_wunsch_gap_incentive 1 --prime_editing_gap_open_penalty -50 --flash_command None --verbosity 3 --amplicon_name Reference --plot_window_size 20 --quantification_window_center -3 --prime_editing_pegRNA_extension_quantification_window_size 5 --min_average_read_quality 0 --fastp_command fastp --prime_editing_pegRNA_scaffold_min_match_length 1 --max_rows_alleles_around_cut_to_plot 50 --amplicon_seq TAAACTACCAGAAGTATCAGTGCTAAAAGTATCCTTTTCTTTCCTACAGATTCCTCCTTATGGCCAACAAGGCCCCAGCGGGTATGGTCAGCAGGGCCAGACTCCATATTACAACCAGCAAAGTCCTCACCCCCAGCAGCAGCAGCCACCCTACTCTCAGCAACCACCATCCCAGACCCCTCATGCTCAACCTTCATATCAGCAGCAGCCTCAGTCTCAGCCACCACAGCTCCAGTCATCTCAGCCTCCATATTCCCAGCAGCCA --flexiguide_homology 80 --trimmomatic_command None --default_min_aln_score 60 --fastq_r1 Sample002_R1.fastq.gz --aln_seed_count 5 --aln_seed_min 2 --guide_seq GGACTTTGCTGGTTGTAATA --needleman_wunsch_aln_matrix_loc EDNAFULL --config_file None --min_bp_quality_or_N 0 --flexiguide_seq None --conversion_nuc_from C --min_frequency_alleles_around_cut_to_plot 0.2 --fastq_r2 Sample002_R2.fastq.gz --prime_editing_gap_extend_penalty 0

[Execution log]:
Computing quantification windows
CRISPRessoPro not installed
Added 0 guides with flexible matching
	Original flexiguides: ['None']
	Found guides: []
	Mismatch locations: []
Processing sequences with fastp...
Read1 before filtering:
total reads: 12102
total bases: 1849211
Q20 bases: 1784716(96.5123%)
Q30 bases: 1766469(95.5256%)

Read2 before filtering:
total reads: 12102
total bases: 1849105
Q20 bases: 1798628(97.2702%)
Q30 bases: 1777246(96.1138%)

Merged and filtered:
total reads: 11721
total bases: 3024892
Q20 bases: 2940909(97.2236%)
Q30 bases: 2914469(96.3495%)

Filtering result:
reads passed filter: 24204
reads failed due to low quality: 0
reads failed due to too many N: 0
reads corrected by overlap analysis: 1079
bases corrected by overlap analysis: 1498

Duplication rate: 68.0714%

Insert size peak (evaluated by paired-end reads): 265

Read pairs merged: 11721
% of original read pairs: 96.8518%
% in reads after filtering: 100%


JSON report: /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/fastp_report.json
HTML report: /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/fastp_report.html

fastp -i Sample002_R1.fastq.gz -I Sample002_R2.fastq.gz --merge --merged_out /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/oet.extendedFrags.fastq.gz --unpaired1 /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/out.notCombined_1.fastq.gz --unpaired2 /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/out.notCombined_2.fastq.gz --overlap_len_require 10 --thread 6 --json /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/fastp_report.json --html /mmfs1/projects/rrc_shared/common/practice_data/CRISPresso/gchlip2_20260708_work/crispresso_out/CRISPRessoBatch_on_crispresso_batch/CRISPResso_on_Sample002/fastp_report.html --disable_adapter_trimming --disable_trim_poly_g --disable_quality_filtering --disable_length_filtering 
fastp v0.23.4, time used: 1 seconds
Done!
Done!
Aligning sequences...
Processing reads; N_TOT_READS: 0 N_COMPUTED_ALN: 0 N_CACHED_ALN: 0 N_COMPUTED_NOTALN: 0 N_CACHED_NOTALN: 0
Processing reads; N_TOT_READS: 10000 N_COMPUTED_ALN: 2813 N_CACHED_ALN: 7071 N_COMPUTED_NOTALN: 52 N_CACHED_NOTALN: 64
Finished reads; N_TOT_READS: 11721 N_COMPUTED_ALN: 3187 N_CACHED_ALN: 8396 N_COMPUTED_NOTALN: 62 N_CACHED_NOTALN: 76
Done!
Quantifying indels/substitutions...
Done!
Calculating allele frequencies...
Done!
Saving processed data...
Making Plots...
Plotting read bar plot
Plotting read class pie chart and bar plot
Begin processing plots for amplicon Reference
Plotting nucleotide quilt across amplicon
Plotting nucleotide distribuition around sgRNA GGACTTTGCTGGTTGTAATA for Reference
Plotting indel size distribution for Reference
Plotting frequency deletions/insertions for Reference
Plotting amplication modifications for Reference
Plotting modification frequency for Reference
Plotting quantification window locations for Reference
Plotting position dependent indel for Reference
Plotting allele distribution around cut for Reference
Done!
Done!
Removing Intermediate files...
 >=1.0% of reads have modifications at the start or end. Total reads: 11583, Irregular reads: 258.
 >=0.2% of substitutions were outside of the quantification window. Total substitutions: 7724, Substitutions outside window: 7160.
Analysis Complete!