Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

detect: --max-reads default #129

Open
nick-youngblut opened this issue Jan 16, 2022 · 1 comment
Open

detect: --max-reads default #129

nick-youngblut opened this issue Jan 16, 2022 · 1 comment

Comments

@nick-youngblut
Copy link

The cli docs for Atropos version 1.1.31 state:

  --max-reads N         Maximum number of reads/pairs to process (no max)

... but the max is actually set to 10000 instead of no max:

        parser.set_defaults(
            max_reads=10000,
            counter_magnitude="K")

So, a atropos detect run with default parameters (and --progress bar):

2022-01-16 07:27:14,174 INFO: Detecting adapters and other potential contaminant sequences based on 12-mers in 10000 reads
  0%|                                                | 10/10000 [00:00<08:54, 18.70it/s]
@nick-youngblut
Copy link
Author

...also the progress bar doesn't seem to work for detect. The entire progress bar output for default parameters is:

0%|                                                | 10/10000 [00:00<07:31, 22.14it/s]

The bar never progresses beyond 0%.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant