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MaWeffm / ReCo

ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs.
MIT License
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IndexError: list index out of range #3

Open Saleh-OM4R opened 8 months ago

Saleh-OM4R commented 8 months ago

Hi, After running this line of code :

r.run(remove_unused_files=True, cores=15)

I've ran into this error : 

  Determine cassette information ...

2024-01-12 18:53:16 INFO: Testing 1728 guides
2024-01-12 18:53:16 INFO: Testing 1728 guides
2024-01-12 18:53:16 INFO: Testing 1728 guides
2024-01-12 18:53:16 INFO: Testing 500 reads
2024-01-12 18:53:16 INFO: Testing 500 reads
2024-01-12 18:53:16 INFO: Testing 500 reads
Determine library direction (1,728 guides in 500 reads): 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 1728/1728 [00:03<00:00, 568.93 guides/s]
2024-01-12 18:53:19 INFO: Forward matches: 0
2024-01-12 18:53:19 INFO: Forward matches: 0
2024-01-12 18:53:19 INFO: Forward matches: 0
2024-01-12 18:53:19 INFO: Forward 5' homologies: []
2024-01-12 18:53:19 INFO: Forward 5' homologies: []
2024-01-12 18:53:19 INFO: Forward 5' homologies: []
2024-01-12 18:53:19 INFO: Forward 3' homologies: []
2024-01-12 18:53:19 INFO: Forward 3' homologies: []
2024-01-12 18:53:19 INFO: Forward 3' homologies: []
2024-01-12 18:53:19 INFO: Reverse matches: 21
2024-01-12 18:53:19 INFO: Reverse matches: 21
2024-01-12 18:53:19 INFO: Reverse matches: 21
2024-01-12 18:53:19 INFO: Reverse 5' homologies: [('TAGCTCTAAAAC', 21)]
2024-01-12 18:53:19 INFO: Reverse 5' homologies: [('TAGCTCTAAAAC', 21)]
2024-01-12 18:53:19 INFO: Reverse 5' homologies: [('TAGCTCTAAAAC', 21)]
2024-01-12 18:53:19 INFO: Reverse 3' homologies: [('GGTGTTTCGTCC', 20), ('GGTGTTTCGGCC', 1)]
2024-01-12 18:53:19 INFO: Reverse 3' homologies: [('GGTGTTTCGTCC', 20), ('GGTGTTTCGGCC', 1)]
2024-01-12 18:53:19 INFO: Reverse 3' homologies: [('GGTGTTTCGTCC', 20), ('GGTGTTTCGGCC', 1)]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/saleh/miniconda3/envs/recoenv/lib/python3.8/site-packages/reco/reco.py", line 94, in run
    for step in sample.run(
  File "/home/saleh/miniconda3/envs/recoenv/lib/python3.8/site-packages/reco/sample.py", line 547, in run
    self.cassette_information_1 = CassetteFinder.run(
  File "/home/saleh/miniconda3/envs/recoenv/lib/python3.8/site-packages/reco/cassette_finder.py", line 85, in run
    return c_finder.find(
  File "/home/saleh/miniconda3/envs/recoenv/lib/python3.8/site-packages/reco/cassette_finder.py", line 113, in find
    return self.find_guides_in_reads(rand_guides, test_reads)
  File "/home/saleh/miniconda3/envs/recoenv/lib/python3.8/site-packages/reco/cassette_finder.py", line 252, in find_guides_in_reads
    reverse_homologies_5.most_common()[1][1]
IndexError: list index out of range`

I don't know exactly what I'm doing wrong, is it a problem with the library file or something else ? Thanks for the package and I would really appreciate any input. Cheers,