error in running --rerender option

[ghost]

Error in --rerender

When I use the command:

screen average_nucleotide_identity.py -v -i all_fna_files_renamed/ -o pyani_out -s 500 -l pyani.log -g --gformat png,pdf,eps,svg --write_excel -m ANIb --rerender

The following error appears:

Traceback (most recent call last):
  File "/home/naiane/anaconda3/bin/average_nucleotide_identity.py", line 814, in <module>
    draw(methods[args.method][1], gfmt)
  File "/home/naiane/anaconda3/bin/average_nucleotide_identity.py", line 637, in draw
    params = pyani_graphics.Params(params_mpl(df)[filestem],
  File "/home/naiane/anaconda3/lib/python3.6/site-packages/pyani/pyani_config.py", line 109, in params_mpl
    return {'ANIb_alignment_lengths': ('afmhot', df.values.min(),
  File "/home/naiane/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py", line 32, in _amin
    return umr_minimum(a, axis, None, out, keepdims, initial)
TypeError: '<=' not supported between instances of 'float' and 'str'

Do you know how to solve it?

Thanks.

[widdowquinn]

Hi,

I'll take a look, but would you be able please to attach a minimal dataset replicating this error message?

Cheers,

L.

[ghost]

.tab file example
ANIb_percentage_identity.zip

[Anenovaes]

Hi,
I was running the pyANI (ANIb) normally, but now I'm having the same problem. How can I solve this?

Thanks.

[baileythegreen]

@widdowquinn The zip file provided above only contains an ANIb_percentage_identity.tab file, which is insufficient to run the command provided.

The error suggests the source is a formatting issue in ANIb_alignment_lengths.tab, where something is being incorrectly treated as a string, however, I am currently unable to reproduce the issue.

@ghost, @Anenovaes I realise you may have moved on, and apologise for the delay. If either of you still have a fileset which produces this issue, could you please provide the full set of output files? Thanks.

If the status of this issue does not change, I would recommend closure.

[widdowquinn]

If the status of this issue does not change, I would recommend closure.

I agree. If we cannot reproduce, we should mark it with the appropriate label and close.