BAM Output issue

[braghavendramicrocrispr-lgtm]

Describe the bug
A clear and concise description of what the bug is.

Expected behavior
A clear and concise description of what you expected to happen.

To reproduce
CRISPResso command to reproduce the behavior.

Debug output
Paste the entire output when you run CRISPResso with the flag --debug.

[braghavendramicrocrispr-lgtm]

First of all, I have to thank you the tool. Its amazing but i see an issue in generation the alignment file (i.e., bam) even after setting the parameter "--bam_output" in CRISPResso2 and terminal throws an error as follows: "Reads processed, now annotating fastq_output file: CRISPResso_output.bam
Traceback (most recent call last):
File "/home/raghavendrab/MCPL_Data/Packages/miniconda3/envs/crispresso2/lib/python3.9/site-packages/CRISPResso2/CRISPRessoCORE.py", line 3500, in main
aln_stats = process_single_fastq_write_bam_out(processed_output_filename, crispresso2_info['bam_output'], bam_header, variantCache, ref_names, refs, args, files_to_remove, OUTPUT_DIRECTORY)
File "/home/raghavendrab/MCPL_Data/Packages/miniconda3/envs/crispresso2/lib/python3.9/site-packages/CRISPResso2/CRISPRessoCORE.py", line 2039, in process_single_fastq_write_bam_out
" ALN_SCORES=" + ('&'.join([str(x) for x in new_variant['aln_scores']])) +
UnboundLocalError: local variable 'new_variant' referenced before assignment

Unexpected error, please check your input.

ERROR: local variable 'new_variant' referenced before assignment"

But ideally without the use of the above parameter "--bam_output", the program the completes the process by generating the other results. Seeking for the support!

Thank You!

[braghavendramicrocrispr-lgtm]

We have used paired-end fastq files for processing using CRISPResso2.

[Colelyman]

Hi @braghavendramicrocrispr-lgtm,
Thank you for using CRISPResso and reporting the issue. This is a known issue and the fix will be included in the next release which we are hoping to ship shortly.

If you would like the fix immediately, you can clone the repo, run pip install . inside the directory (with your existing conda environment activated) and then --bam_output should work for you. Please let us know if you run into any further issues or this doesn't work for you.

Thanks,
Cole

[kclem]

This issue has been resolved in v2.3.4. Please let us know if you're still having problems.