Numpy Error about crispresso2 HOT 6 OPEN

@ahrimj21 Sorry about this error.

Can you run with the --debug flag and paste the output here?

from crispresso2.

Traceback (most recent call last):
File "/opt/anaconda3/envs/crispresso2_env/lib/python3.8/site-packages/CRISPResso2/CRISPRessoCORE.py", line 3210, in main
mod_pcts.append(np.concatenate((['Insertions'], np.array(all_insertion_count_vectors[ref_name]).astype(np.float)/tot)))
File "/opt/anaconda3/envs/crispresso2_env/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'float'.
np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
CRITICAL @ Fri, 21 Jun 2024 21:47:01:
Traceback (most recent call last):
File "/opt/anaconda3/envs/crispresso2_env/lib/python3.8/site-packages/CRISPResso2/CRISPRessoCORE.py", line 3210, in main
mod_pcts.append(np.concatenate((['Insertions'], np.array(all_insertion_count_vectors[ref_name]).astype(np.float)/tot)))
File "/opt/anaconda3/envs/crispresso2_env/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'float'.
np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

CRITICAL @ Fri, 21 Jun 2024 21:47:01:
Unexpected error, please check your input.

ERROR: module 'numpy' has no attribute 'float'.
np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

WARNING:root:CRISPResso command failed (return value 255) on batch #4: "CRISPResso -o /Users/ahrim/CRISPRessoBatch_on_2024-05-17_crispressobatch_input-Red --name A05 --trimmomatic_command trimmomatic --amplicon_name 11 --needleman_wunsch_aln_matrix_loc EDNAFULL --coding_seq AGTACCCAAAGGCAAGTGGAACAGCTCTAATGGGGTTGAAGAAAAGGAGACTTGGGTGGAAGAGGATGAACTGTTTCAAGTTCAGG --needleman_wunsch_gap_incentive 1 --debug --max_paired_end_reads_overlap 100 --min_bp_quality_or_N 0 --amplicon_seq GCGAACCTCGATTGTGGTCACAACGGGACAGGAAGGAGTACAGGGCCAAGAGTGAGCCAAGACCAGAATCTGGGACAATCCAGGGTGAATTTGTTTTATACCTGTGCTCTCCTTGATCTCCCCTCAGAGTACCCAAAGGCAAGTGGAACAGCTCTAATGGGGTTGAAGAAAAGGAGACTTGGGTGGAAGAGGATGAACTGTTTCAAGTTCAGGGTAAGCAGAAGATTCTCCTTGGCCTCTTCTTGATGCTTGCTGAAGTACAGATGCGTG --flexiguide_homology 80 --fastq_r2 /Users/ahrim/Desktop/Summer_Lab/Ahrim_SummerWork/Data/fastqs/Red/DH20240417RedV4A05_S321_L001_R2_001.fastq.gz --plot_window_size 20 --flash_command flash --conversion_nuc_to T --max_rows_alleles_around_cut_to_plot 50 --min_paired_end_reads_overlap 10 --quantification_window_size 15 --prime_editing_pegRNA_extension_quantification_window_size 5 --exclude_bp_from_left 15 --min_frequency_alleles_around_cut_to_plot 0.2 --needleman_wunsch_gap_extend -2 --exclude_bp_from_right 15 --needleman_wunsch_gap_open -20 --n_processes 1 --guide_seq GGTTGAAGAAAAGGAGACTT --aln_seed_min 2 --fastq_r1 /Users/ahrim/Desktop/Summer_Lab/Ahrim_SummerWork/Data/fastqs/Red/DH20240417RedV4A05_S321_L001_R1_001.fastq.gz --prime_editing_pegRNA_scaffold_min_match_length 1 --conversion_nuc_from C --aln_seed_count 5 --min_average_read_quality 0 --aln_seed_len 10 --min_single_bp_quality 0 --quantification_window_center "-3" --default_min_aln_score 60"

from crispresso2.

Sorry that you are running into this error, would you mind sharing the version of numpy you have installed? I think this may be due to having version 2.0.0 of numpy installed. We will fix this in the next release, but in the meantime everything should work if you install version 1.26.4 of numpy. Let us know if this works or not!

from crispresso2.

I have numpy version 1.24.3 installed.

from crispresso2.

Thanks, do you know what version of CRISPResso you have installed? It looks like the latest version (v2.3.1) has this bug fixed https://github.com/pinellolab/CRISPResso2/blob/master/CRISPResso2/CRISPRessoCORE.py#L3764

Please let us know if you still see this error on v2.3.1!

from crispresso2.

I have CRISPResso version 2.2.8! I will try installing the latest version right now and let you know. Thank you

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