CRISPResso version 2.3.4
[Command used]:
/var/www/webapps/CRISPRessoWEB/.pixi/envs/dev/bin/CRISPResso --fastq_r1 prime_editor.fastq.gz --amplicon_seq ACGTCTCATATGCCCCTTGGCAGTCATCTTAGTCATTACCTGAGGTGTTCGTTGTAACTCATATAAACTGAGTTCCCATGTTTTGCTTAATGGTTGAGTTCCGTTTGTCTGCACAGCCTGAGACATTGCTGGAAATAAAGAAGAGAGAAAAACAATTTTAGTATTTGGAAGGGAAGTGCTATGGTCTGAATGTATGTGTCCCACCAAAATTCCTACGT --prime_editing_pegRNA_spacer_seq GTCATCTTAGTCATTACCTG --prime_editing_pegRNA_extension_seq AACGAACACCTCATGTAATGACTAAGATG --prime_editing_nicking_guide_seq CTCAACCATTAAGCAAAACAT --prime_editing_pegRNA_scaffold_seq GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC --write_cleaned_report --place_report_in_output_folder

[Execution log]:
CRISPRessoPro v1.0.1 installed
Computing quantification windows
Added 0 guides with flexible matching
	Original flexiguides: ['None']
	Found guides: []
	Mismatch locations: []
Added 0 guides with flexible matching
	Original flexiguides: ['None']
	Found guides: []
	Mismatch locations: []
Counting reads in input
Counting reads after preprocessing...
Aligning sequences...
Finished reading fastq file; 5557 unique reads found of 25000 total reads found 
Processing Reads; 0 Completed out of 5557 Unique Reads
Finished reads; N_TOT_READS: 25000 N_COMPUTED_ALN: 5471 N_CACHED_ALN: 19440 N_COMPUTED_NOTALN: 86 N_CACHED_NOTALN: 3
Done!
Quantifying indels/substitutions...
Done!
Calculating allele frequencies...
Done!
Saving processed data...
Making Plots...
Done!
Removing Intermediate files...
Disproportionate percentages of reads were aligned to amplicon: Reference, Percent of aligned reads aligned to this amplicon: 57.59%.
Disproportionate percentages of reads were aligned to amplicon: Prime-edited, Percent of aligned reads aligned to this amplicon: 38.94%.
Disproportionate percentages of reads were aligned to amplicon: Scaffold-incorporated, Percent of aligned reads aligned to this amplicon: 2.12%.
>=1.0% of reads have modifications at the start or end. Total reads: 24911, Irregular reads: 24907.
>=0.2% of substitutions were outside of the quantification window. Total substitutions: 6550, Substitutions outside window: 5668.
Pro report written to CRISPResso_on_prime_editor/CRISPResso2_report.html
                                                                               
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Analysis Complete!