ValueError when creating experiment plots and tables

[ShanSabri]

• crispector version: conda version
• Python version: 3.7
• Operating System: Ubuntu 18.04.5

Description

 CCCCC  RRRRRR  IIIII  SSSSS  PPPPPP  EEEEEEE  CCCCC  TTTTTTT  OOOOO  RRRRRR
CC    C RR   RR  III  SS      PP   PP EE      CC    C   TTT   OO   OO RR   RR
CC      RRRRRR   III   SSSSS  PPPPPP  EEEEE   CC        TTT   OO   OO RRRRRR
CC    C RR  RR   III       SS PP      EE      CC    C   TTT   OO   OO RR  RR
 CCCCC  RR   RR IIIII  SSSSS  PP      EEEEEEE  CCCCC    TTT    OOOOO  RR   RR

              CRISPR/CAS9 Off-Target Analysis From NGS Data

2021-07-07 17:15:35,380 INFO     fastp for treatment - Run (may take a few minutes).
2021-07-07 17:15:38,277 INFO     fastp for treatment - Done.
2021-07-07 17:15:38,278 INFO     fastp for mock - Run (may take a few minutes).
2021-07-07 17:15:40,969 INFO     fastp for mock - Done.
2021-07-07 17:15:42,194 INFO     Assigning reads to target amplicons for treatment - Start assigning 221,402 reads - May take a few minutes
2021-07-07 17:15:51,876 INFO     Assigning reads to target amplicons for treatment - 43,409 reads weren't matched (19.61% of all reads)
2021-07-07 17:15:52,410 WARNING  The following read has 16317 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:15:52,427 WARNING  The following read has 4800 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:15:52,443 WARNING  The following read has 2079 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:15:52,460 WARNING  The following read has 982 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCTTAACGAGGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-07 17:15:52,476 WARNING  The following read has 880 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:15:52,491 WARNING  The following read has 718 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-07 17:15:52,506 WARNING  The following read has 546 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-07 17:15:52,522 WARNING  The following read has 510 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCTTCGAGGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-07 17:15:52,522 INFO     Assigning reads to target amplicons for treatment - Done
2021-07-07 17:15:53,640 INFO     Assigning reads to target amplicons for mock - Start assigning 206,609 reads - May take a few minutes
2021-07-07 17:16:01,367 INFO     Assigning reads to target amplicons for mock - 29,051 reads weren't matched (14.06% of all reads)
2021-07-07 17:16:01,643 WARNING  The following read has 9928 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCTTACGAGGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-07 17:16:01,660 WARNING  The following read has 6489 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:16:01,677 WARNING  The following read has 2453 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:16:01,693 WARNING  The following read has 991 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-07 17:16:01,694 INFO     Assigning reads to target amplicons for mock - Done
2021-07-07 17:16:02,515 INFO     Alignment for site_1_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:02,728 INFO     Alignment for site_1_treatment - Done.
2021-07-07 17:16:03,600 INFO     Alignment for site_1_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:03,853 INFO     Alignment for site_1_mock - Done.
2021-07-07 17:16:06,128 INFO     Alignment for site_2_treatment - 1 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:06,529 INFO     Alignment for site_2_treatment - Done.
2021-07-07 17:16:08,391 INFO     Alignment for site_2_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:08,720 INFO     Alignment for site_2_mock - Done.
2021-07-07 17:16:09,230 INFO     Alignment for site_3_treatment - 7 reads were filtered out (0.06% of all reads)
2021-07-07 17:16:09,386 INFO     Alignment for site_3_treatment - Done.
2021-07-07 17:16:10,358 INFO     Alignment for site_3_mock - 5 reads were filtered out (0.02% of all reads)
2021-07-07 17:16:10,652 INFO     Alignment for site_3_mock - Done.
2021-07-07 17:16:12,375 INFO     Alignment for site_4_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:12,700 INFO     Alignment for site_4_treatment - Done.
2021-07-07 17:16:14,440 INFO     Alignment for site_4_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:14,768 INFO     Alignment for site_4_mock - Done.
2021-07-07 17:16:15,710 INFO     Alignment for site_5_treatment - 27 reads were filtered out (0.11% of all reads)
2021-07-07 17:16:15,973 INFO     Alignment for site_5_treatment - Done.
2021-07-07 17:16:16,961 INFO     Alignment for site_5_mock - 17 reads were filtered out (0.09% of all reads)
2021-07-07 17:16:17,237 INFO     Alignment for site_5_mock - Done.
2021-07-07 17:16:17,799 INFO     Alignment for site_6_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:17,990 INFO     Alignment for site_6_treatment - Done.
2021-07-07 17:16:18,757 INFO     Alignment for site_6_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:19,015 INFO     Alignment for site_6_mock - Done.
2021-07-07 17:16:19,068 INFO     Alignment for site_7_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:19,092 INFO     Alignment for site_7_treatment - Done.
2021-07-07 17:16:19,121 INFO     Alignment for site_7_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:19,136 INFO     Alignment for site_7_mock - Done.
2021-07-07 17:16:20,542 INFO     Alignment for site_8_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:20,806 INFO     Alignment for site_8_treatment - Done.
2021-07-07 17:16:22,442 INFO     Alignment for site_8_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:22,748 INFO     Alignment for site_8_mock - Done.
2021-07-07 17:16:24,049 INFO     Alignment for site_9_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:24,329 INFO     Alignment for site_9_treatment - Done.
2021-07-07 17:16:25,972 INFO     Alignment for site_9_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:26,324 INFO     Alignment for site_9_mock - Done.
2021-07-07 17:16:26,656 INFO     Alignment for site_10_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:26,768 INFO     Alignment for site_10_treatment - Done.
2021-07-07 17:16:27,233 INFO     Alignment for site_10_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:27,389 INFO     Alignment for site_10_mock - Done.
2021-07-07 17:16:28,340 INFO     Alignment for site_11_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:28,599 INFO     Alignment for site_11_treatment - Done.
2021-07-07 17:16:29,641 INFO     Alignment for site_11_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:29,927 INFO     Alignment for site_11_mock - Done.
2021-07-07 17:16:30,863 INFO     Alignment for site_12_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:31,128 INFO     Alignment for site_12_treatment - Done.
2021-07-07 17:16:32,281 INFO     Alignment for site_12_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-07 17:16:32,606 INFO     Alignment for site_12_mock - Done.
2021-07-07 17:16:32,607 INFO     Convert alignment tables to algorithm input
2021-07-07 17:16:32,607 INFO     Site target_site - Discarded from evaluation due to low number of reads (treatment=0, mock=0).
2021-07-07 17:16:35,127 INFO     Site site_7 - Discarded from evaluation due to low number of reads (treatment=213, mock=102).
2021-07-07 17:16:37,158 WARNING  On-target site was discarded from evaluation. Will use default q parameter (= 0.93) from config file for the Bayesian NHEJ inference (check CRISPECTOR paper for more details).
2021-07-07 17:16:37,158 INFO     Start Evaluating editing activity for all sites
2021-07-07 17:16:41,206 INFO     Evaluating editing activity for all sites - Done!
2021-07-07 17:16:41,206 INFO     Translocations - Run HG tests
2021-07-07 17:16:41,209 INFO     Start creating experiment plots and tables
2021-07-07 17:16:55,178 INFO     Traceback (most recent call last):
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/crispector_main.py", line 146, in run
    min_editing_activity, translocation_p_value, output, donor)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/report/visualization_and_output.py", line 116, in create_experiment_output
    plot_editing_activity(result_df, confidence_interval, editing_threshold, html_d, output)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/report/visualization_and_output.py", line 790, in plot_editing_activity
    fig, axes = plt.subplots(nrows=plot_num, ncols=1, figsize=(fig_w, fig_h), tight_layout=True)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
    return func(*args, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1442, in subplots
    gridspec_kw=gridspec_kw)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
    return func(*args, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/figure.py", line 907, in subplots
    gs = self.add_gridspec(nrows, ncols, figure=self, **gridspec_kw)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/figure.py", line 1405, in add_gridspec
    gs = GridSpec(nrows=nrows, ncols=ncols, figure=self, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/gridspec.py", line 399, in __init__
    height_ratios=height_ratios)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/gridspec.py", line 50, in __init__
    f"Number of rows must be a positive integer, not {nrows}")
ValueError: Number of rows must be a positive integer, not 0

2021-07-07 17:16:55,178 ERROR    Unknown Error. Please contact crispector package author

What I Did

#!/bin/bash
crispector -t_r1 raw_data/IL6196/IL6196_R1.fastq.gz -t_r2 raw_data/IL6196/IL6196_R2.fastq.gz -m_r1 raw_data/IL6195/IL6195_R1.fastq.gz -m_r2 raw_data/IL6195/IL6195_R2.fastq.gz -c IL6196_config.csv -o IL6196_out

Any ideas on how to get this to properly run would be great!

[ShanSabri]

Additional information from the output log (crispector_main.log):

2021-07-07 17:19:00,321 INFO     fastp for treatment - Run (may take a few minutes).
Read1 before filtering:
total reads: 224869
total bases: 33730350
Q20 bases: 33114793(98.1751%)
Q30 bases: 32926810(97.6178%)

Read2 before filtering:
total reads: 224869
total bases: 33730350
Q20 bases: 33005955(97.8524%)
Q30 bases: 32608011(96.6726%)

Merged and filtered:
total reads: 221768
total bases: 42437051
Q20 bases: 41810913(98.5245%)
Q30 bases: 41592906(98.0108%)

Filtering result:
reads passed filter: 446470
reads failed due to low quality: 3176
reads failed due to too many N: 92
reads failed due to too short: 0
reads with adapter trimmed: 10050
bases trimmed due to adapters: 184045
reads corrected by overlap analysis: 10542
bases corrected by overlap analysis: 22644

Duplication rate: 77.6357%

Insert size peak (evaluated by paired-end reads): 180

Read pairs merged: 221768
% of original read pairs: 98.621%
% in reads after filtering: 100%

JSON report: IL6196_out/crispector_output/treatment_fastp/fastp.json
HTML report: IL6196_out/crispector_output/treatment_fastp/fastp.html

fastp -i raw_data/IL6196/IL6196_R1.fastq.gz -I raw_data/IL6196/IL6196_R2.fastq.gz -o IL6196_out/crispector_output/treatment_fastp/r1_filtered_reads.fastq -O IL6196_out/crispector_output/treatment_fastp/r2_filtered_reads.fastq -m --merged_out IL6196_out/crispector_output/treatment_fastp/merged_reads.fastq -j IL6196_out/crispector_output/treatment_fastp/fastp.json -h IL6196_out/crispector_output/treatment_fastp/fastp.html --length_required 40 -w 2 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT 
fastp v0.20.1, time used: 3 seconds
2021-07-07 17:19:03,255 INFO     fastp for treatment - Done.
2021-07-07 17:19:03,255 INFO     fastp for mock - Run (may take a few minutes).
Read1 before filtering:
total reads: 209232
total bases: 31384800
Q20 bases: 30907202(98.4783%)
Q30 bases: 30742634(97.9539%)

Read2 before filtering:
total reads: 209232
total bases: 31384800
Q20 bases: 30746879(97.9674%)
Q30 bases: 30408295(96.8886%)

Merged and filtered:
total reads: 206920
total bases: 39201936
Q20 bases: 38682659(98.6754%)
Q30 bases: 38485708(98.173%)

Filtering result:
reads passed filter: 415520
reads failed due to low quality: 2874
reads failed due to too many N: 70
reads failed due to too short: 0
reads with adapter trimmed: 6
bases trimmed due to adapters: 58
reads corrected by overlap analysis: 8350
bases corrected by overlap analysis: 17603

Duplication rate: 78.0157%

Insert size peak (evaluated by paired-end reads): 175

Read pairs merged: 206920
% of original read pairs: 98.895%
% in reads after filtering: 100%

[iamit87]

Hi @ShanSabri, If your data can be shared, I’ll be happy to reproduce the error on my machine. (You can share via google drive to idoamit98@gmail.com) If not, I’ll try to debug the issue with a more detailed log. Please rerun with ‘—verbose’ flag and send me the log

[ShanSabri]

Hi @iamit87 - Sure thing - I've sent some test data your way to debug.

Also posted below is the log with verbose mode:

$ crispector -t_r1 raw_data/IL6196/IL6196_R1.fastq.gz -t_r2 raw_data/IL6196/IL6196_R2.fastq.gz -m_r1 raw_data/IL6195/IL6195_R1.fastq.gz -m_r2 raw_data/IL6195/IL6195_R2.fastq.gz -c IL6196_config.csv -o IL6196_out --verbose 

/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  BiopythonDeprecationWarning,
2021-07-09 15:46:16,147 DEBUG    Command used:
 /home/ubuntu/.Anaconda3/envs/crispector_env/bin/crispector -t_r1 raw_data/IL6196/IL6196_R1.fastq.gz -t_r2 raw_data/IL6196/IL6196_R2.fastq.gz -m_r1 raw_data/IL6195/IL6195_R1.fastq.gz -m_r2 raw_data/IL6195/IL6195_R2.fastq.gz -c IL6196_config.csv -o IL6196_out --verbose
2021-07-09 15:46:16,209 DEBUG    fastp for treatment - Command fastp -i raw_data/IL6196/IL6196_R1.fastq.gz -I raw_data/IL6196/IL6196_R2.fastq.gz -o IL6196_out/crispector_output/treatment_fastp/r1_filtered_reads.fastq -O IL6196_out/crispector_output/treatment_fastp/r2_filtered_reads.fastq -m --merged_out IL6196_out/crispector_output/treatment_fastp/merged_reads.fastq -j IL6196_out/crispector_output/treatment_fastp/fastp.json -h IL6196_out/crispector_output/treatment_fastp/fastp.html --length_required 40 -w 2 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT >> IL6196_out/crispector_output/crispector_main.log 2>&1
2021-07-09 15:46:16,209 INFO     fastp for treatment - Run (may take a few minutes).
2021-07-09 15:46:19,118 INFO     fastp for treatment - Done.
2021-07-09 15:46:19,118 DEBUG    fastp for mock - Command fastp -i raw_data/IL6195/IL6195_R1.fastq.gz -I raw_data/IL6195/IL6195_R2.fastq.gz -o IL6196_out/crispector_output/mock_fastp/r1_filtered_reads.fastq -O IL6196_out/crispector_output/mock_fastp/r2_filtered_reads.fastq -m --merged_out IL6196_out/crispector_output/mock_fastp/merged_reads.fastq -j IL6196_out/crispector_output/mock_fastp/fastp.json -h IL6196_out/crispector_output/mock_fastp/fastp.html --length_required 40 -w 2 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT >> IL6196_out/crispector_output/crispector_main.log 2>&1
2021-07-09 15:46:19,119 INFO     fastp for mock - Run (may take a few minutes).
2021-07-09 15:46:21,847 INFO     fastp for mock - Done.
2021-07-09 15:46:23,093 INFO     Assigning reads to target amplicons for treatment - Start assigning 221,402 reads - May take a few minutes
2021-07-09 15:46:25,638 DEBUG    Search possible Translocations for 43,671 reads. May take a few minutes
2021-07-09 15:46:32,793 DEBUG    Site matching for ambiguous reads and Translocations Search - Done.
2021-07-09 15:46:32,809 INFO     Assigning reads to target amplicons for treatment - 43,409 reads weren't matched (19.61% of all reads)
2021-07-09 15:46:33,339 WARNING  The following read has 16317 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:33,356 WARNING  The following read has 4800 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:33,373 WARNING  The following read has 2079 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:33,389 WARNING  The following read has 982 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCTTAACGAGGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-09 15:46:33,406 WARNING  The following read has 880 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:33,420 WARNING  The following read has 718 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-09 15:46:33,436 WARNING  The following read has 546 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-09 15:46:33,452 WARNING  The following read has 510 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCTTCGAGGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-09 15:46:33,452 INFO     Assigning reads to target amplicons for treatment - Done
2021-07-09 15:46:34,593 INFO     Assigning reads to target amplicons for mock - Start assigning 206,609 reads - May take a few minutes
2021-07-09 15:46:37,007 DEBUG    Search possible Translocations for 29,185 reads. May take a few minutes
2021-07-09 15:46:42,321 DEBUG    Site matching for ambiguous reads and Translocations Search - Done.
2021-07-09 15:46:42,335 INFO     Assigning reads to target amplicons for mock - 29,051 reads weren't matched (14.06% of all reads)
2021-07-09 15:46:42,610 WARNING  The following read has 9928 repetitions, but it doesn't match any site!This read is most similar to reference site target_site. Please check amplicon sequences correctness. read=ACTCAGACACCCTCTCCTGTGTGCAGGACGTGCCGAATGTTCAGGTGCAATGAGAATGAGCCATGCTTGGCTTACGAGGGCAATCTGGCCCATCAAGTGGCCTTCGCCTCTGGGAGTAACAAAAATGCACTTCAAAATAGCTTCTGTAATCAAGCTGCATGGG
2021-07-09 15:46:42,627 WARNING  The following read has 6489 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:42,644 WARNING  The following read has 2453 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:42,661 WARNING  The following read has 991 repetitions, but it doesn't match any site!This read is most similar to reference site site_7. Please check amplicon sequences correctness. read=CTGGTAATGGGATCACTTTACCTGTTTATGTGATTTTCTTTGGCAATTATTAATTGGGCTTTTTTTTTTTTAGGAAAGAGAGACATGCTTGGCTTACCTTGAGTAACAGGGGTTTATTGTAAATAAATGAATGTGAGGTTTTAATCCCTAGATGATGAGCCTTCATGAAG
2021-07-09 15:46:42,661 INFO     Assigning reads to target amplicons for mock - Done
2021-07-09 15:46:42,750 DEBUG    Alignment - Start alignment for all reads
2021-07-09 15:46:42,751 DEBUG    Alignment for site_1_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:43,485 INFO     Alignment for site_1_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:43,487 DEBUG    Alignment for site_1_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:46:43,487 DEBUG    Alignment for site_1_treatment - Start shift modifications into cut-site.
2021-07-09 15:46:43,593 DEBUG    Alignment for site_1_treatment - Shift modifications into cut-site done.
2021-07-09 15:46:43,701 INFO     Alignment for site_1_treatment - Done.
2021-07-09 15:46:43,701 DEBUG    Alignment for site_1_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:44,575 INFO     Alignment for site_1_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:44,576 DEBUG    Alignment for site_1_mock - Needleman-Wunsch alignment done.
2021-07-09 15:46:44,576 DEBUG    Alignment for site_1_mock - Start shift modifications into cut-site.
2021-07-09 15:46:44,700 DEBUG    Alignment for site_1_mock - Shift modifications into cut-site done.
2021-07-09 15:46:44,828 INFO     Alignment for site_1_mock - Done.
2021-07-09 15:46:44,829 DEBUG    Alignment for site_2_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:47,104 INFO     Alignment for site_2_treatment - 1 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:47,106 DEBUG    Alignment for site_2_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:46:47,106 DEBUG    Alignment for site_2_treatment - Start shift modifications into cut-site.
2021-07-09 15:46:47,302 DEBUG    Alignment for site_2_treatment - Shift modifications into cut-site done.
2021-07-09 15:46:47,508 INFO     Alignment for site_2_treatment - Done.
2021-07-09 15:46:47,508 DEBUG    Alignment for site_2_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:49,373 INFO     Alignment for site_2_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:49,374 DEBUG    Alignment for site_2_mock - Needleman-Wunsch alignment done.
2021-07-09 15:46:49,374 DEBUG    Alignment for site_2_mock - Start shift modifications into cut-site.
2021-07-09 15:46:49,536 DEBUG    Alignment for site_2_mock - Shift modifications into cut-site done.
2021-07-09 15:46:49,704 INFO     Alignment for site_2_mock - Done.
2021-07-09 15:46:49,704 DEBUG    Alignment for site_3_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:50,215 INFO     Alignment for site_3_treatment - 7 reads were filtered out (0.06% of all reads)
2021-07-09 15:46:50,217 DEBUG    Alignment for site_3_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:46:50,218 DEBUG    Alignment for site_3_treatment - Start shift modifications into cut-site.
2021-07-09 15:46:50,293 DEBUG    Alignment for site_3_treatment - Shift modifications into cut-site done.
2021-07-09 15:46:50,373 INFO     Alignment for site_3_treatment - Done.
2021-07-09 15:46:50,374 DEBUG    Alignment for site_3_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:51,347 INFO     Alignment for site_3_mock - 5 reads were filtered out (0.02% of all reads)
2021-07-09 15:46:51,349 DEBUG    Alignment for site_3_mock - Needleman-Wunsch alignment done.
2021-07-09 15:46:51,349 DEBUG    Alignment for site_3_mock - Start shift modifications into cut-site.
2021-07-09 15:46:51,493 DEBUG    Alignment for site_3_mock - Shift modifications into cut-site done.
2021-07-09 15:46:51,643 INFO     Alignment for site_3_mock - Done.
2021-07-09 15:46:51,644 DEBUG    Alignment for site_4_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:53,370 INFO     Alignment for site_4_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:53,372 DEBUG    Alignment for site_4_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:46:53,372 DEBUG    Alignment for site_4_treatment - Start shift modifications into cut-site.
2021-07-09 15:46:53,531 DEBUG    Alignment for site_4_treatment - Shift modifications into cut-site done.
2021-07-09 15:46:53,696 INFO     Alignment for site_4_treatment - Done.
2021-07-09 15:46:53,697 DEBUG    Alignment for site_4_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:55,439 INFO     Alignment for site_4_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:55,440 DEBUG    Alignment for site_4_mock - Needleman-Wunsch alignment done.
2021-07-09 15:46:55,440 DEBUG    Alignment for site_4_mock - Start shift modifications into cut-site.
2021-07-09 15:46:55,601 DEBUG    Alignment for site_4_mock - Shift modifications into cut-site done.
2021-07-09 15:46:55,769 INFO     Alignment for site_4_mock - Done.
2021-07-09 15:46:55,769 DEBUG    Alignment for site_5_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:56,712 INFO     Alignment for site_5_treatment - 27 reads were filtered out (0.11% of all reads)
2021-07-09 15:46:56,715 DEBUG    Alignment for site_5_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:46:56,715 DEBUG    Alignment for site_5_treatment - Start shift modifications into cut-site.
2021-07-09 15:46:56,843 DEBUG    Alignment for site_5_treatment - Shift modifications into cut-site done.
2021-07-09 15:46:56,977 INFO     Alignment for site_5_treatment - Done.
2021-07-09 15:46:56,978 DEBUG    Alignment for site_5_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:57,968 INFO     Alignment for site_5_mock - 17 reads were filtered out (0.09% of all reads)
2021-07-09 15:46:57,969 DEBUG    Alignment for site_5_mock - Needleman-Wunsch alignment done.
2021-07-09 15:46:57,969 DEBUG    Alignment for site_5_mock - Start shift modifications into cut-site.
2021-07-09 15:46:58,105 DEBUG    Alignment for site_5_mock - Shift modifications into cut-site done.
2021-07-09 15:46:58,247 INFO     Alignment for site_5_mock - Done.
2021-07-09 15:46:58,247 DEBUG    Alignment for site_6_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:58,811 INFO     Alignment for site_6_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:58,813 DEBUG    Alignment for site_6_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:46:58,813 DEBUG    Alignment for site_6_treatment - Start shift modifications into cut-site.
2021-07-09 15:46:58,906 DEBUG    Alignment for site_6_treatment - Shift modifications into cut-site done.
2021-07-09 15:46:59,004 INFO     Alignment for site_6_treatment - Done.
2021-07-09 15:46:59,004 DEBUG    Alignment for site_6_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:46:59,771 INFO     Alignment for site_6_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:46:59,772 DEBUG    Alignment for site_6_mock - Needleman-Wunsch alignment done.
2021-07-09 15:46:59,772 DEBUG    Alignment for site_6_mock - Start shift modifications into cut-site.
2021-07-09 15:46:59,900 DEBUG    Alignment for site_6_mock - Shift modifications into cut-site done.
2021-07-09 15:47:00,032 INFO     Alignment for site_6_mock - Done.
2021-07-09 15:47:00,032 DEBUG    Alignment for site_7_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:00,085 INFO     Alignment for site_7_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:00,087 DEBUG    Alignment for site_7_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:47:00,087 DEBUG    Alignment for site_7_treatment - Start shift modifications into cut-site.
2021-07-09 15:47:00,097 DEBUG    Alignment for site_7_treatment - Shift modifications into cut-site done.
2021-07-09 15:47:00,110 INFO     Alignment for site_7_treatment - Done.
2021-07-09 15:47:00,110 DEBUG    Alignment for site_7_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:00,140 INFO     Alignment for site_7_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:00,141 DEBUG    Alignment for site_7_mock - Needleman-Wunsch alignment done.
2021-07-09 15:47:00,141 DEBUG    Alignment for site_7_mock - Start shift modifications into cut-site.
2021-07-09 15:47:00,147 DEBUG    Alignment for site_7_mock - Shift modifications into cut-site done.
2021-07-09 15:47:00,156 INFO     Alignment for site_7_mock - Done.
2021-07-09 15:47:00,156 DEBUG    Alignment for site_8_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:01,564 INFO     Alignment for site_8_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:01,566 DEBUG    Alignment for site_8_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:47:01,566 DEBUG    Alignment for site_8_treatment - Start shift modifications into cut-site.
2021-07-09 15:47:01,697 DEBUG    Alignment for site_8_treatment - Shift modifications into cut-site done.
2021-07-09 15:47:01,829 INFO     Alignment for site_8_treatment - Done.
2021-07-09 15:47:01,829 DEBUG    Alignment for site_8_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:03,467 INFO     Alignment for site_8_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:03,468 DEBUG    Alignment for site_8_mock - Needleman-Wunsch alignment done.
2021-07-09 15:47:03,469 DEBUG    Alignment for site_8_mock - Start shift modifications into cut-site.
2021-07-09 15:47:03,620 DEBUG    Alignment for site_8_mock - Shift modifications into cut-site done.
2021-07-09 15:47:03,774 INFO     Alignment for site_8_mock - Done.
2021-07-09 15:47:03,775 DEBUG    Alignment for site_9_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:05,076 INFO     Alignment for site_9_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:05,077 DEBUG    Alignment for site_9_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:47:05,077 DEBUG    Alignment for site_9_treatment - Start shift modifications into cut-site.
2021-07-09 15:47:05,215 DEBUG    Alignment for site_9_treatment - Shift modifications into cut-site done.
2021-07-09 15:47:05,357 INFO     Alignment for site_9_treatment - Done.
2021-07-09 15:47:05,357 DEBUG    Alignment for site_9_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:07,001 INFO     Alignment for site_9_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:07,002 DEBUG    Alignment for site_9_mock - Needleman-Wunsch alignment done.
2021-07-09 15:47:07,002 DEBUG    Alignment for site_9_mock - Start shift modifications into cut-site.
2021-07-09 15:47:07,176 DEBUG    Alignment for site_9_mock - Shift modifications into cut-site done.
2021-07-09 15:47:07,355 INFO     Alignment for site_9_mock - Done.
2021-07-09 15:47:07,356 DEBUG    Alignment for site_10_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:07,688 INFO     Alignment for site_10_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:07,689 DEBUG    Alignment for site_10_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:47:07,689 DEBUG    Alignment for site_10_treatment - Start shift modifications into cut-site.
2021-07-09 15:47:07,744 DEBUG    Alignment for site_10_treatment - Shift modifications into cut-site done.
2021-07-09 15:47:07,801 INFO     Alignment for site_10_treatment - Done.
2021-07-09 15:47:07,802 DEBUG    Alignment for site_10_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:08,268 INFO     Alignment for site_10_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:08,269 DEBUG    Alignment for site_10_mock - Needleman-Wunsch alignment done.
2021-07-09 15:47:08,269 DEBUG    Alignment for site_10_mock - Start shift modifications into cut-site.
2021-07-09 15:47:08,345 DEBUG    Alignment for site_10_mock - Shift modifications into cut-site done.
2021-07-09 15:47:08,424 INFO     Alignment for site_10_mock - Done.
2021-07-09 15:47:08,424 DEBUG    Alignment for site_11_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:09,376 INFO     Alignment for site_11_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:09,378 DEBUG    Alignment for site_11_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:47:09,378 DEBUG    Alignment for site_11_treatment - Start shift modifications into cut-site.
2021-07-09 15:47:09,504 DEBUG    Alignment for site_11_treatment - Shift modifications into cut-site done.
2021-07-09 15:47:09,637 INFO     Alignment for site_11_treatment - Done.
2021-07-09 15:47:09,638 DEBUG    Alignment for site_11_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:10,681 INFO     Alignment for site_11_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:10,682 DEBUG    Alignment for site_11_mock - Needleman-Wunsch alignment done.
2021-07-09 15:47:10,682 DEBUG    Alignment for site_11_mock - Start shift modifications into cut-site.
2021-07-09 15:47:10,820 DEBUG    Alignment for site_11_mock - Shift modifications into cut-site done.
2021-07-09 15:47:10,966 INFO     Alignment for site_11_mock - Done.
2021-07-09 15:47:10,967 DEBUG    Alignment for site_12_treatment - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:11,903 INFO     Alignment for site_12_treatment - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:11,904 DEBUG    Alignment for site_12_treatment - Needleman-Wunsch alignment done.
2021-07-09 15:47:11,904 DEBUG    Alignment for site_12_treatment - Start shift modifications into cut-site.
2021-07-09 15:47:12,035 DEBUG    Alignment for site_12_treatment - Shift modifications into cut-site done.
2021-07-09 15:47:12,169 INFO     Alignment for site_12_treatment - Done.
2021-07-09 15:47:12,169 DEBUG    Alignment for site_12_mock - Start Needleman-Wunsch alignment for all reads.
2021-07-09 15:47:13,323 INFO     Alignment for site_12_mock - 0 reads were filtered out (0.00% of all reads)
2021-07-09 15:47:13,325 DEBUG    Alignment for site_12_mock - Needleman-Wunsch alignment done.
2021-07-09 15:47:13,325 DEBUG    Alignment for site_12_mock - Start shift modifications into cut-site.
2021-07-09 15:47:13,485 DEBUG    Alignment for site_12_mock - Shift modifications into cut-site done.
2021-07-09 15:47:13,650 INFO     Alignment for site_12_mock - Done.
2021-07-09 15:47:13,651 INFO     Convert alignment tables to algorithm input
2021-07-09 15:47:13,652 INFO     Site target_site - Discarded from evaluation due to low number of reads (treatment=0, mock=0).
2021-07-09 15:47:13,992 DEBUG    Site site_1 - Converted. Number of reads (treatment=18635, mock=17415).
2021-07-09 15:47:14,549 DEBUG    Site site_2 - Converted. Number of reads (treatment=22523, mock=13573).
2021-07-09 15:47:14,907 DEBUG    Site site_3 - Converted. Number of reads (treatment=11030, mock=22434).
2021-07-09 15:47:15,444 DEBUG    Site site_4 - Converted. Number of reads (treatment=17850, mock=13982).
2021-07-09 15:47:15,841 DEBUG    Site site_5 - Converted. Number of reads (treatment=23941, mock=19466).
2021-07-09 15:47:16,170 DEBUG    Site site_6 - Converted. Number of reads (treatment=17905, mock=20719).
2021-07-09 15:47:16,170 INFO     Site site_7 - Discarded from evaluation due to low number of reads (treatment=213, mock=102).
2021-07-09 15:47:16,670 DEBUG    Site site_8 - Converted. Number of reads (treatment=10074, mock=10256).
2021-07-09 15:47:17,139 DEBUG    Site site_9 - Converted. Number of reads (treatment=18830, mock=20900).
2021-07-09 15:47:17,332 DEBUG    Site site_10 - Converted. Number of reads (treatment=5637, mock=7713).
2021-07-09 15:47:17,740 DEBUG    Site site_11 - Converted. Number of reads (treatment=15330, mock=14135).
2021-07-09 15:47:18,190 DEBUG    Site site_12 - Converted. Number of reads (treatment=15988, mock=16840).
2021-07-09 15:47:18,190 WARNING  On-target site was discarded from evaluation. Will use default q parameter (= 0.93) from config file for the Bayesian NHEJ inference (check CRISPECTOR paper for more details).
2021-07-09 15:47:18,190 INFO     Start Evaluating editing activity for all sites
2021-07-09 15:47:18,469 DEBUG    Site site_1 - Editing activity is 0.02
2021-07-09 15:47:19,033 DEBUG    Site site_2 - Editing activity is 0.00
2021-07-09 15:47:19,286 DEBUG    Site site_3 - Editing activity is 0.00
2021-07-09 15:47:19,864 DEBUG    Site site_4 - Editing activity is 0.00
2021-07-09 15:47:20,200 DEBUG    Site site_5 - Editing activity is 0.00
2021-07-09 15:47:20,446 DEBUG    Site site_6 - Editing activity is 0.00
2021-07-09 15:47:20,986 DEBUG    Site site_8 - Editing activity is 0.00
2021-07-09 15:47:21,357 DEBUG    Site site_9 - Editing activity is 0.00
2021-07-09 15:47:21,503 DEBUG    Site site_10 - Editing activity is 0.00
2021-07-09 15:47:21,865 DEBUG    Site site_11 - Editing activity is 0.00
2021-07-09 15:47:22,243 DEBUG    Site site_12 - Editing activity is 0.01
2021-07-09 15:47:22,245 INFO     Evaluating editing activity for all sites - Done!
2021-07-09 15:47:22,245 INFO     Translocations - Run HG tests
2021-07-09 15:47:22,248 DEBUG    Translocations - HG test - Done!
2021-07-09 15:47:22,248 INFO     Start creating experiment plots and tables
2021-07-09 15:47:40,402 INFO     Traceback (most recent call last):
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/crispector_main.py", line 146, in run
    min_editing_activity, translocation_p_value, output, donor)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/report/visualization_and_output.py", line 116, in create_experiment_output
    plot_editing_activity(result_df, confidence_interval, editing_threshold, html_d, output)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/report/visualization_and_output.py", line 790, in plot_editing_activity
    fig, axes = plt.subplots(nrows=plot_num, ncols=1, figsize=(fig_w, fig_h), tight_layout=True)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
    return func(*args, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1442, in subplots
    gridspec_kw=gridspec_kw)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
    return func(*args, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/figure.py", line 907, in subplots
    gs = self.add_gridspec(nrows, ncols, figure=self, **gridspec_kw)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/figure.py", line 1405, in add_gridspec
    gs = GridSpec(nrows=nrows, ncols=ncols, figure=self, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/gridspec.py", line 399, in __init__
    height_ratios=height_ratios)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/gridspec.py", line 50, in __init__
    f"Number of rows must be a positive integer, not {nrows}")
ValueError: Number of rows must be a positive integer, not 0

2021-07-09 15:47:40,402 ERROR    Unknown Error. Please contact crispector package author

[iamit87]

Hi @ShanSabri,

I found the issue. CRISPECTOR crashes if there are 0 reads for the on-target site. We will fix this issue next version. I reviewed your experiment configuration and found out that the on-target site and site number 7 had a partial amplicon reference. As a result CRISPECTOR couldn't assign the correct reads to these sites. I fixed the amplicon reference and CRISPECTOR worked as properly. the on-target has 98% editing activity with very low numbers of off-target editing activity (nice!).

I've upload the report and the correct configuration file to your shared directory.

[ShanSabri]

Hi @iamit87 -- I'm getting a similar error for another sample I'm trying to process. In this case there is no on-target sequence. Here's the verbose output:

2021-11-11 00:58:56,134 DEBUG    Command used:
 /home/ubuntu/.Anaconda3/envs/crispector_env/bin/crispector -t_r1 raw_data/IL54269/IL54269_R1.fastq.gz -t_r2 raw_data/IL54269/IL54269_R2.fastq.gz -m_r1 raw_data/IL54270/IL54270_R1.fastq.gz -m_r2 raw_data/IL54270/IL54270_R2.fastq.gz -c rhAmp_CRISPR_10_config.csv -o IL54269_out --verbose
2021-11-11 00:58:56,183 DEBUG    fastp for treatment - Command fastp -i raw_data/IL54269/IL54269_R1.fastq.gz -I raw_data/IL54269/IL54269_R2.fastq.gz -o IL54269_out/crispector_output/treatment_fastp/r1_filtered_reads.fastq -O IL54269_out/crispector_output/treatment_fastp/r2_filtered_reads.fastq -m --merged_out IL54269_out/crispector_output/treatment_fastp/merged_reads.fastq -j IL54269_out/crispector_output/treatment_fastp/fastp.json -h IL54269_out/crispector_output/treatment_fastp/fastp.html --length_required 40 -w 2 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT >> IL54269_out/crispector_output/crispector_main.log 2>&1
2021-11-11 00:58:56,183 INFO     fastp for treatment - Run (may take a few minutes).
2021-11-11 00:59:00,663 INFO     fastp for treatment - Done.
2021-11-11 00:59:00,663 DEBUG    fastp for mock - Command fastp -i raw_data/IL54270/IL54270_R1.fastq.gz -I raw_data/IL54270/IL54270_R2.fastq.gz -o IL54269_out/crispector_output/mock_fastp/r1_filtered_reads.fastq -O IL54269_out/crispector_output/mock_fastp/r2_filtered_reads.fastq -m --merged_out IL54269_out/crispector_output/mock_fastp/merged_reads.fastq -j IL54269_out/crispector_output/mock_fastp/fastp.json -h IL54269_out/crispector_output/mock_fastp/fastp.html --length_required 40 -w 2 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT >> IL54269_out/crispector_output/crispector_main.log 2>&1
2021-11-11 00:59:00,663 INFO     fastp for mock - Run (may take a few minutes).
2021-11-11 00:59:05,108 INFO     fastp for mock - Done.
2021-11-11 00:59:06,726 INFO     Assigning reads to target amplicons for treatment - Start assigning 274,170 reads - May take a few minutes
2021-11-11 00:59:10,852 DEBUG    Search possible Translocations for 45 reads. May take a few minutes
2021-11-11 00:59:10,891 DEBUG    Site matching for ambiguous reads and Translocations Search - Done.
2021-11-11 00:59:10,906 INFO     Assigning reads to target amplicons for treatment - 23 reads weren't matched (0.01% of all reads)
2021-11-11 00:59:10,910 INFO     Assigning reads to target amplicons for treatment - Done
2021-11-11 00:59:12,127 INFO     Assigning reads to target amplicons for mock - Start assigning 215,204 reads - May take a few minutes
2021-11-11 00:59:15,506 DEBUG    Search possible Translocations for 47 reads. May take a few minutes
2021-11-11 00:59:15,562 DEBUG    Site matching for ambiguous reads and Translocations Search - Done.
2021-11-11 00:59:15,574 INFO     Assigning reads to target amplicons for mock - 19 reads weren't matched (0.01% of all reads)
2021-11-11 00:59:15,577 INFO     Assigning reads to target amplicons for mock - Done
2021-11-11 00:59:15,677 DEBUG    Alignment - Start alignment for all reads
2021-11-11 00:59:15,678 DEBUG    Alignment for Elevation_8_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:25,854 INFO     Alignment for Elevation_8_treatment - 15 reads were filtered out (0.01% of all reads)
2021-11-11 00:59:25,857 DEBUG    Alignment for Elevation_8_treatment - Needleman-Wunsch alignment done.
2021-11-11 00:59:25,857 DEBUG    Alignment for Elevation_8_treatment - Start shift modifications into cut-site.
2021-11-11 00:59:26,820 DEBUG    Alignment for Elevation_8_treatment - Shift modifications into cut-site done.
2021-11-11 00:59:27,815 INFO     Alignment for Elevation_8_treatment - Done.
2021-11-11 00:59:27,815 DEBUG    Alignment for Elevation_8_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:32,680 INFO     Alignment for Elevation_8_mock - 3 reads were filtered out (0.01% of all reads)
2021-11-11 00:59:32,682 DEBUG    Alignment for Elevation_8_mock - Needleman-Wunsch alignment done.
2021-11-11 00:59:32,682 DEBUG    Alignment for Elevation_8_mock - Start shift modifications into cut-site.
2021-11-11 00:59:33,139 DEBUG    Alignment for Elevation_8_mock - Shift modifications into cut-site done.
2021-11-11 00:59:33,612 INFO     Alignment for Elevation_8_mock - Done.
2021-11-11 00:59:33,613 DEBUG    Alignment for iGuide_6_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:39,508 INFO     Alignment for iGuide_6_treatment - 5 reads were filtered out (0.02% of all reads)
2021-11-11 00:59:39,510 DEBUG    Alignment for iGuide_6_treatment - Needleman-Wunsch alignment done.
2021-11-11 00:59:39,510 DEBUG    Alignment for iGuide_6_treatment - Start shift modifications into cut-site.
2021-11-11 00:59:40,815 DEBUG    Alignment for iGuide_6_treatment - Shift modifications into cut-site done.
2021-11-11 00:59:42,218 INFO     Alignment for iGuide_6_treatment - Done.
2021-11-11 00:59:42,218 DEBUG    Alignment for iGuide_6_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:48,569 INFO     Alignment for iGuide_6_mock - 5 reads were filtered out (0.02% of all reads)
2021-11-11 00:59:48,572 DEBUG    Alignment for iGuide_6_mock - Needleman-Wunsch alignment done.
2021-11-11 00:59:48,572 DEBUG    Alignment for iGuide_6_mock - Start shift modifications into cut-site.
2021-11-11 00:59:49,978 DEBUG    Alignment for iGuide_6_mock - Shift modifications into cut-site done.
2021-11-11 00:59:51,493 INFO     Alignment for iGuide_6_mock - Done.
2021-11-11 00:59:51,494 DEBUG    Alignment for iGuide_24_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:53,589 INFO     Alignment for iGuide_24_treatment - 0 reads were filtered out (0.00% of all reads)
2021-11-11 00:59:53,590 DEBUG    Alignment for iGuide_24_treatment - Needleman-Wunsch alignment done.
2021-11-11 00:59:53,590 DEBUG    Alignment for iGuide_24_treatment - Start shift modifications into cut-site.
2021-11-11 00:59:53,772 DEBUG    Alignment for iGuide_24_treatment - Shift modifications into cut-site done.
2021-11-11 00:59:53,965 INFO     Alignment for iGuide_24_treatment - Done.
2021-11-11 00:59:53,965 DEBUG    Alignment for iGuide_24_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:57,826 INFO     Alignment for iGuide_24_mock - 0 reads were filtered out (0.00% of all reads)
2021-11-11 00:59:57,828 DEBUG    Alignment for iGuide_24_mock - Needleman-Wunsch alignment done.
2021-11-11 00:59:57,829 DEBUG    Alignment for iGuide_24_mock - Start shift modifications into cut-site.
2021-11-11 00:59:58,163 DEBUG    Alignment for iGuide_24_mock - Shift modifications into cut-site done.
2021-11-11 00:59:58,514 INFO     Alignment for iGuide_24_mock - Done.
2021-11-11 00:59:58,515 DEBUG    Alignment for iGuide_35_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 00:59:58,939 INFO     Alignment for iGuide_35_treatment - 7 reads were filtered out (0.09% of all reads)
2021-11-11 00:59:58,940 DEBUG    Alignment for iGuide_35_treatment - Needleman-Wunsch alignment done.
2021-11-11 00:59:58,940 DEBUG    Alignment for iGuide_35_treatment - Start shift modifications into cut-site.
2021-11-11 00:59:58,995 DEBUG    Alignment for iGuide_35_treatment - Shift modifications into cut-site done.
2021-11-11 00:59:59,053 INFO     Alignment for iGuide_35_treatment - Done.
2021-11-11 00:59:59,053 DEBUG    Alignment for iGuide_35_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:00,042 INFO     Alignment for iGuide_35_mock - 41 reads were filtered out (0.18% of all reads)
2021-11-11 01:00:00,045 DEBUG    Alignment for iGuide_35_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:00,045 DEBUG    Alignment for iGuide_35_mock - Start shift modifications into cut-site.
2021-11-11 01:00:00,170 DEBUG    Alignment for iGuide_35_mock - Shift modifications into cut-site done.
2021-11-11 01:00:00,301 INFO     Alignment for iGuide_35_mock - Done.
2021-11-11 01:00:00,301 DEBUG    Alignment for iGuide_39_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:00,907 INFO     Alignment for iGuide_39_treatment - 1 reads were filtered out (0.01% of all reads)
2021-11-11 01:00:00,908 DEBUG    Alignment for iGuide_39_treatment - Needleman-Wunsch alignment done.
2021-11-11 01:00:00,908 DEBUG    Alignment for iGuide_39_treatment - Start shift modifications into cut-site.
2021-11-11 01:00:00,971 DEBUG    Alignment for iGuide_39_treatment - Shift modifications into cut-site done.
2021-11-11 01:00:01,038 INFO     Alignment for iGuide_39_treatment - Done.
2021-11-11 01:00:01,038 DEBUG    Alignment for iGuide_39_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:02,116 INFO     Alignment for iGuide_39_mock - 6 reads were filtered out (0.03% of all reads)
2021-11-11 01:00:02,117 DEBUG    Alignment for iGuide_39_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:02,117 DEBUG    Alignment for iGuide_39_mock - Start shift modifications into cut-site.
2021-11-11 01:00:02,229 DEBUG    Alignment for iGuide_39_mock - Shift modifications into cut-site done.
2021-11-11 01:00:02,345 INFO     Alignment for iGuide_39_mock - Done.
2021-11-11 01:00:02,345 DEBUG    Alignment for iGuide_46_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:11,824 INFO     Alignment for iGuide_46_treatment - 3 reads were filtered out (0.00% of all reads)
2021-11-11 01:00:11,826 DEBUG    Alignment for iGuide_46_treatment - Needleman-Wunsch alignment done.
2021-11-11 01:00:11,826 DEBUG    Alignment for iGuide_46_treatment - Start shift modifications into cut-site.
2021-11-11 01:00:12,714 DEBUG    Alignment for iGuide_46_treatment - Shift modifications into cut-site done.
2021-11-11 01:00:13,640 INFO     Alignment for iGuide_46_treatment - Done.
2021-11-11 01:00:13,641 DEBUG    Alignment for iGuide_46_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:17,500 INFO     Alignment for iGuide_46_mock - 1 reads were filtered out (0.00% of all reads)
2021-11-11 01:00:17,502 DEBUG    Alignment for iGuide_46_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:17,502 DEBUG    Alignment for iGuide_46_mock - Start shift modifications into cut-site.
2021-11-11 01:00:17,862 DEBUG    Alignment for iGuide_46_mock - Shift modifications into cut-site done.
2021-11-11 01:00:18,239 INFO     Alignment for iGuide_46_mock - Done.
2021-11-11 01:00:18,239 DEBUG    Alignment for iGuide_56_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:18,276 INFO     Alignment for iGuide_56_treatment - 1 reads were filtered out (1.69% of all reads)
2021-11-11 01:00:18,277 DEBUG    Alignment for iGuide_56_treatment - Needleman-Wunsch alignment done.
2021-11-11 01:00:18,277 DEBUG    Alignment for iGuide_56_treatment - Start shift modifications into cut-site.
2021-11-11 01:00:18,286 DEBUG    Alignment for iGuide_56_treatment - Shift modifications into cut-site done.
2021-11-11 01:00:18,294 INFO     Alignment for iGuide_56_treatment - Done.
2021-11-11 01:00:18,295 DEBUG    Alignment for iGuide_56_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:18,349 INFO     Alignment for iGuide_56_mock - 0 reads were filtered out (0.00% of all reads)
2021-11-11 01:00:18,350 DEBUG    Alignment for iGuide_56_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:18,350 DEBUG    Alignment for iGuide_56_mock - Start shift modifications into cut-site.
2021-11-11 01:00:18,357 DEBUG    Alignment for iGuide_56_mock - Shift modifications into cut-site done.
2021-11-11 01:00:18,368 INFO     Alignment for iGuide_56_mock - Done.
2021-11-11 01:00:18,368 DEBUG    Alignment for iGuide_64_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:19,174 INFO     Alignment for iGuide_64_treatment - 9 reads were filtered out (0.03% of all reads)
2021-11-11 01:00:19,176 DEBUG    Alignment for iGuide_64_treatment - Needleman-Wunsch alignment done.
2021-11-11 01:00:19,176 DEBUG    Alignment for iGuide_64_treatment - Start shift modifications into cut-site.
2021-11-11 01:00:19,301 DEBUG    Alignment for iGuide_64_treatment - Shift modifications into cut-site done.
2021-11-11 01:00:19,430 INFO     Alignment for iGuide_64_treatment - Done.
2021-11-11 01:00:19,430 DEBUG    Alignment for iGuide_64_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:20,766 INFO     Alignment for iGuide_64_mock - 19 reads were filtered out (0.04% of all reads)
2021-11-11 01:00:20,768 DEBUG    Alignment for iGuide_64_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:20,768 DEBUG    Alignment for iGuide_64_mock - Start shift modifications into cut-site.
2021-11-11 01:00:20,976 DEBUG    Alignment for iGuide_64_mock - Shift modifications into cut-site done.
2021-11-11 01:00:21,186 INFO     Alignment for iGuide_64_mock - Done.
2021-11-11 01:00:21,186 DEBUG    Alignment for iGuide_81_treatment - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:21,201 INFO     Alignment for iGuide_81_treatment - 7 reads were filtered out (36.84% of all reads)
2021-11-11 01:00:21,202 DEBUG    Alignment for iGuide_81_treatment - Needleman-Wunsch alignment done.
2021-11-11 01:00:21,202 DEBUG    Alignment for iGuide_81_treatment - Start shift modifications into cut-site.
2021-11-11 01:00:21,204 DEBUG    Alignment for iGuide_81_treatment - Shift modifications into cut-site done.
2021-11-11 01:00:21,210 INFO     Alignment for iGuide_81_treatment - Done.
2021-11-11 01:00:21,210 DEBUG    Alignment for iGuide_81_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:21,229 INFO     Alignment for iGuide_81_mock - 15 reads were filtered out (39.47% of all reads)
2021-11-11 01:00:21,231 DEBUG    Alignment for iGuide_81_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:21,231 DEBUG    Alignment for iGuide_81_mock - Start shift modifications into cut-site.
2021-11-11 01:00:21,233 DEBUG    Alignment for iGuide_81_mock - Shift modifications into cut-site done.
2021-11-11 01:00:21,239 INFO     Alignment for iGuide_81_mock - Done.
2021-11-11 01:00:21,239 DEBUG    Alignment for iGuide_85_mock - Start Needleman-Wunsch alignment for all reads.
2021-11-11 01:00:21,247 INFO     Alignment for iGuide_85_mock - 0 reads were filtered out (0.00% of all reads)
2021-11-11 01:00:21,248 DEBUG    Alignment for iGuide_85_mock - Needleman-Wunsch alignment done.
2021-11-11 01:00:21,248 DEBUG    Alignment for iGuide_85_mock - Start shift modifications into cut-site.
2021-11-11 01:00:21,250 DEBUG    Alignment for iGuide_85_mock - Shift modifications into cut-site done.
2021-11-11 01:00:21,255 INFO     Alignment for iGuide_85_mock - Done.
2021-11-11 01:00:21,256 INFO     Convert alignment tables to algorithm input
2021-11-11 01:00:23,690 DEBUG    Site Elevation_8 - Converted. Number of reads (treatment=102571, mock=35659).
2021-11-11 01:00:31,076 DEBUG    Site iGuide_6 - Converted. Number of reads (treatment=28744, mock=29316).
2021-11-11 01:00:31,845 DEBUG    Site iGuide_24 - Converted. Number of reads (treatment=16048, mock=31712).
2021-11-11 01:00:32,095 DEBUG    Site iGuide_35 - Converted. Number of reads (treatment=7811, mock=22158).
2021-11-11 01:00:32,330 DEBUG    Site iGuide_39 - Converted. Number of reads (treatment=10476, mock=22155).
2021-11-11 01:00:34,331 DEBUG    Site iGuide_46 - Converted. Number of reads (treatment=78445, mock=23534).
2021-11-11 01:00:34,332 INFO     Site iGuide_56 - Discarded from evaluation due to low number of reads (treatment=58, mock=99).
2021-11-11 01:00:34,802 DEBUG    Site iGuide_64 - Converted. Number of reads (treatment=29934, mock=50420).
2021-11-11 01:00:34,803 INFO     Site iGuide_81 - Discarded from evaluation due to low number of reads (treatment=12, mock=23).
2021-11-11 01:00:34,803 INFO     Site iGuide_85 - Discarded from evaluation due to low number of reads (treatment=0, mock=19).
2021-11-11 01:00:34,803 WARNING  Experiment doesn't have on-target site. Will use default q parameter (= 0.93) from config file for the Bayesian NHEJ inference (check CRISPECTOR paper for more details).
2021-11-11 01:00:34,803 INFO     Start Evaluating editing activity for all sites
2021-11-11 01:00:38,409 DEBUG    Site Elevation_8 - Editing activity is 0.00
2021-11-11 01:00:51,299 DEBUG    Site iGuide_6 - Editing activity is 0.01
2021-11-11 01:00:51,737 DEBUG    Site iGuide_24 - Editing activity is 0.00
2021-11-11 01:00:51,837 DEBUG    Site iGuide_35 - Editing activity is 0.00
2021-11-11 01:00:51,947 DEBUG    Site iGuide_39 - Editing activity is 0.00
2021-11-11 01:00:54,725 DEBUG    Site iGuide_46 - Editing activity is 0.00
2021-11-11 01:00:54,993 DEBUG    Site iGuide_64 - Editing activity is 0.00
2021-11-11 01:00:54,996 INFO     Evaluating editing activity for all sites - Done!
2021-11-11 01:00:54,996 INFO     Translocations - Run HG tests
2021-11-11 01:00:54,997 DEBUG    Translocations - HG test - Done!
2021-11-11 01:00:54,998 INFO     Start creating experiment plots and tables
2021-11-11 01:01:14,326 INFO     Traceback (most recent call last):
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/crispector_main.py", line 146, in run
    min_editing_activity, translocation_p_value, output, donor)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/report/visualization_and_output.py", line 116, in create_experiment_output
    plot_editing_activity(result_df, confidence_interval, editing_threshold, html_d, output)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/crispector/report/visualization_and_output.py", line 790, in plot_editing_activity
    fig, axes = plt.subplots(nrows=plot_num, ncols=1, figsize=(fig_w, fig_h), tight_layout=True)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
    return func(*args, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1442, in subplots
    gridspec_kw=gridspec_kw)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
    return func(*args, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/figure.py", line 907, in subplots
    gs = self.add_gridspec(nrows, ncols, figure=self, **gridspec_kw)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/figure.py", line 1405, in add_gridspec
    gs = GridSpec(nrows=nrows, ncols=ncols, figure=self, **kwargs)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/gridspec.py", line 399, in __init__
    height_ratios=height_ratios)
  File "/home/ubuntu/.Anaconda3/envs/crispector_env/lib/python3.7/site-packages/matplotlib/gridspec.py", line 50, in __init__
    f"Number of rows must be a positive integer, not {nrows}")
ValueError: Number of rows must be a positive integer, not 0

2021-11-11 01:01:14,326 ERROR    Unknown Error. Please contact crispector package author

Anything stick out to you as a clear error? Seems to be computing the correct editing activity?

[ShanSabri]

Solved by using the --min_editing_activity 0