Minimal reproduction:
$ echo $'>fails\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' > fails.fasta \
&& docker run -it --rm --platform=linux/amd64 -w "$(pwd)" -v "$(pwd):$(pwd)" \
community.wave.seqera.io/library/cryptkeeper_transtermhp:e544e0104f88e78a \
cryptkeeper -i fails.fasta -o repo
[2026-06-09 18:48:00,397] Cryptkeeper: Running RhoTermPredict
[2026-06-09 18:48:00,398] Cryptkeeper: Running TransTerm
[2026-06-09 18:48:00,493] Cryptkeeper: Running Promoter Calculator
[2026-06-09 18:48:00,502] Cryptkeeper: Running ORF prediction
[2026-06-09 18:48:00,504] Cryptkeeper: Running RBS prediction
[2026-06-09 18:48:00,562] Cryptkeeper: Exporting data
Traceback (most recent call last):
File "/opt/conda/bin/cryptkeeper", line 10, in <module>
sys.exit(main())
~~~~^^
File "/opt/conda/lib/python3.13/site-packages/cryptkeeper/cryptkeeper.py", line 149, in main
_ = make_plot(
result,
...<2 lines>...
show_small=show_small,
)
File "/opt/conda/lib/python3.13/site-packages/cryptkeeper/plot.py", line 1076, in make_plot
layout = column(
layout, *tables, styles={"margin": "0 auto", "align-items": "center"}
)
File "/opt/conda/lib/python3.13/site-packages/bokeh/layouts.py", line 152, in column
_handle_child_sizing(_children, sizing_mode, widget="column")
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.13/site-packages/bokeh/layouts.py", line 679, in _handle_child_sizing
raise ValueError(f"Only LayoutDOM items can be inserted into a {widget}. Tried to insert: {item} of type {type(item)}")
ValueError: Only LayoutDOM items can be inserted into a column. Tried to insert: Promoters of type <class 'str'>I expected that input would be valid, cryptkeeper would exit without an error, and I'd get the html page with a plot.
I am running cryptkeeper v1.0.2 under python v3.13.13 full docker image details
Minimal reproduction:
I expected that input would be valid, cryptkeeper would exit without an error, and I'd get the html page with a plot.
I am running cryptkeeper v1.0.2 under python v3.13.13 full docker image details