No output files

[Wang-Jing-NZ]

We got this error message:
[2024-12-11 05:57:12] WARNING: Folder <melon/barcode14.fastq> exists. Files will be overwritten.
[2024-12-11 05:57:12] INFO: Estimating genome copies ...
[2024-12-11 06:01:00] INFO: ... found 182.625 copies of genomes (bacteria: 182.625; archaea: 0).
[2024-12-11 06:01:00] INFO: Assigning taxonomy ...
[2024-12-11 06:03:05] INFO: Reassigning taxonomy ...
Traceback (most recent call last):
File "/opt/conda/envs/melon/bin/melon", line 10, in
sys.exit(cli())
^^^^^
File "/opt/conda/envs/melon/lib/python3.12/site-packages/melon/cli.py", line 132, in cli
run(opt)
File "/opt/conda/envs/melon/lib/python3.12/site-packages/melon/cli.py", line 186, in run
GenomeProfiler(file, opt.db, opt.output, opt.threads).run(
File "/opt/conda/envs/melon/lib/python3.12/site-packages/melon/melon.py", line 292, in run
self.run_em(max_iterations=max_iterations, epsilon=epsilon)
File "/opt/conda/envs/melon/lib/python3.12/site-packages/melon/melon.py", line 231, in run_em
assignments.append(np.where(p_read == p_read.max())[0].tolist())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Calling nonzero on 0d arrays is not allowed. Use np.atleast_1d(scalar).nonzero() instead. If the context of this error is of the form arr[nonzero(cond)], just use arr[cond].

Guess the array is empty but the code isn't able to handle it?
Can you look into this? Many thanks.

[xinehc]

Hi,

This error likely occurs due to a bug triggered by pure isolates of certain uncommon/unambiguous species and NumPy>=1.17.

This patch (e07636d) should fix the issue. Thank you for reporting this bug and let me know if you still encounter the error.