CRISPResso version 2.3.4
[Command used]:
/var/www/webapps/CRISPRessoWEB/.pixi/envs/default/bin/CRISPResso -r1 nhej.r1.fastq.gz -r2 nhej.r2.fastq.gz -a AATGTCCCCCAATGGGAAGTTCATCTGGCACTGCCCACAGGTGAGGAGGTCATGATCCCCTTCTGGAGCTCCCAACGGGCCGTGGTCTGGTTCATCATCTGTAAGAATGGCTTCAAGAGGCTCGGCTGTGGTT -n nhej --write_cleaned_report --place_report_in_output_folder --use_matplotlib

[Execution log]:
CRISPRessoPro v1.0.1 installed
Computing quantification windows
Added 0 guides with flexible matching
	Original flexiguides: ['None']
	Found guides: []
	Mismatch locations: []
Counting reads in input
Processing sequences with fastp...
Read1 before filtering:
total reads: 25000
total bases: 3203270
Q20 bases: 3107259(97.0027%)
Q30 bases: 3093007(96.5578%)
Q40 bases: 10(0.000312181%)

Read2 before filtering:
total reads: 25000
total bases: 3198956
Q20 bases: 3063300(95.7594%)
Q30 bases: 3045686(95.2087%)
Q40 bases: 1(3.12602e-05%)

Merged and filtered:
total reads: 24554
total bases: 3129999
Q20 bases: 3057250(97.6758%)
Q30 bases: 3045067(97.2865%)
Q40 bases: 10(0.000319489%)

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 --out1 CRISPResso_on_nhej/out.notCombined_1.fastq.gz --out2 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 v1.3.0, time used: 1 seconds
Done!
Done!
Counting reads after preprocessing...
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...
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.
Pro report written to CRISPResso_on_nhej/CRISPResso2_report.html
                                                                               
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Analysis Complete!