CRISPResso version 2.3.2
[Command used]:
/opt/conda/bin/CRISPResso -r1 nhej.r1.fastq.gz -r2 nhej.r2.fastq.gz -a AATGTCCCCCAATGGGAAGTTCATCTGGCACTGCCCACAGGTGAGGAGGTCATGATCCCCTTCTGGAGCTCCCAACGGGCCGTGGTCTGGTTCATCATCTGTAAGAATGGCTTCAAGAGGCTCGGCTGTGGTT -n nhej --write_cleaned_report --place_report_in_output_folder

[Execution log]:
CRISPRessoPro not installed
Computing quantification windows
Added 0 guides with flexible matching
	Original flexiguides: ['None']
	Found guides: []
	Mismatch locations: []
Processing sequences with fastp...
Read1 before filtering:
total reads: 25000
total bases: 3203270
Q20 bases: 3107259(97.0027%)
Q30 bases: 3093007(96.5578%)

Read2 before filtering:
total reads: 25000
total bases: 3198956
Q20 bases: 3063300(95.7594%)
Q30 bases: 3045686(95.2087%)

Merged and filtered:
total reads: 24554
total bases: 3129999
Q20 bases: 3057250(97.6758%)
Q30 bases: 3045067(97.2865%)

Filtering result:
reads passed filter: 50000
reads failed due to low quality: 0
reads failed due to too many N: 0
reads corrected by overlap analysis: 1086
bases corrected by overlap analysis: 1718

Duplication rate: 79.36%

Insert size peak (evaluated by paired-end reads): 133

Read pairs merged: 24554
% of original read pairs: 98.216%
% in reads after filtering: 100%


JSON report: CRISPResso_on_nhej/fastp_report.json
HTML report: CRISPResso_on_nhej/fastp_report.html

fastp -i nhej.r1.fastq.gz -I nhej.r2.fastq.gz --merge --merged_out CRISPResso_on_nhej/out.extendedFrags.fastq.gz --unpaired1 CRISPResso_on_nhej/out.notCombined_1.fastq.gz --unpaired2 CRISPResso_on_nhej/out.notCombined_2.fastq.gz --overlap_len_require 10 --thread 1 --json CRISPResso_on_nhej/fastp_report.json --html CRISPResso_on_nhej/fastp_report.html --disable_adapter_trimming --disable_trim_poly_g --disable_quality_filtering --disable_length_filtering 
fastp v0.24.0, time used: 2 seconds
Done!
Done!
Aligning sequences...
Finished reading fastq file; 3460 unique reads found of 24554 total reads found 
Processing Reads; 0 Completed out of 3460 Unique Reads
Finished reads; N_TOT_READS: 24554 N_COMPUTED_ALN: 3355 N_CACHED_ALN: 20989 N_COMPUTED_NOTALN: 105 N_CACHED_NOTALN: 105
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 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
Done!
Done!
Removing Intermediate files...
 >=1.0% of reads have modifications at the start or end. Total reads: 24344, Irregular reads: 458.
 >=0.2% of substitutions were outside of the quantification window. Total substitutions: 9093, Substitutions outside window: 1051.
Analysis Complete!
                                                                               
                                        _                                      
                                       '  )                                    
                                       .-'                                     
                                      (____                                    
                                   C)|     \                                   
                                     \     /                                   
                                      \___/                                    

