CRISPResso version 2.0.40
[Command used]:
CRISPResso -o CRISPRessoBatch_on_batch --name FANCF_BE3 --needleman_wunsch_gap_extend -2 --aln_seed_count 5 --amplicon_name Reference --amplicon_seq CATTGCAGAGAGGCGTATCATTTCGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCC --max_rows_alleles_around_cut_to_plot 50 --prime_editing_pegRNA_extension_quantification_window_size 5 --fastq_r1 SRR3305545.fastq.gz --quantification_window_size 20 --quantification_window_center -10 --trimmomatic_command trimmomatic --conversion_nuc_from C --min_bp_quality_or_N 0 --base_editor_output --default_min_aln_score 60 --needleman_wunsch_gap_incentive 1 --min_paired_end_reads_overlap 10 --plot_window_size 20 --prime_editing_pegRNA_scaffold_min_match_length 1 --aln_seed_min 2 --aln_seed_len 10 --needleman_wunsch_gap_open -20 --max_paired_end_reads_overlap 100 --guide_seq GGAATCCCTTCTGCAGCACC --place_report_in_output_folder --conversion_nuc_to T --flexiguide_homology 80 --flash_command flash --min_single_bp_quality 0 --exclude_bp_from_left 15 --needleman_wunsch_aln_matrix_loc EDNAFULL --min_average_read_quality 0 --min_frequency_alleles_around_cut_to_plot 0.2 --exclude_bp_from_right 15 --write_cleaned_report

[Execution log]:
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: 2816 N_CACHED_ALN: 5106 N_COMPUTED_NOTALN: 550 N_CACHED_NOTALN: 1528
Processing reads; N_TOT_READS: 20000 N_COMPUTED_ALN: 5352 N_CACHED_ALN: 10638 N_COMPUTED_NOTALN: 890 N_CACHED_NOTALN: 3120
Finished reads; N_TOT_READS: 25000 N_COMPUTED_ALN: 6575 N_CACHED_ALN: 13517 N_COMPUTED_NOTALN: 1020 N_CACHED_NOTALN: 3888
Done!
Quantifying indels/substitutions...
Done!
Calculating allele frequencies...
Done!
Saving processed data...
Making Plots...
Done!
Removing Intermediate files...
Analysis Complete!