Error phylophlan_assign_sgbs.py

Hallo,

I am using Phylophlan version 3.0.68. I receive this error :

File “/usr/local/lib/python3.12/site-packages/phylophlan/phylophlan_assign_sgbs.py”, line 934, in phylophlan_metagenomic
bash: File: command not found
Singularity> prefiltering_pasting(args.output_prefix, args.input_extension, chocophlan_list, os.path.basename(args.database), verbose=True)
bash: syntax error near unexpected token args.output_prefix,' Singularity> File "/usr/local/lib/python3.12/site-packages/phylophlan/phylophlan_assign_sgbs.py", line 611, in prefiltering_pasting bash: File: command not found Singularity> info('Inputs pasted in {}s\n'.format(int(t1 - t0))) bash: syntax error near unexpected token ‘Inputs pasted in {}s\n’.format’
Singularity> ^^
bash: ^^: command not found
Singularity> NameError: name ‘t0’ is not defined. Did you mean: ‘t1’?

what’s the problem?

thank you very much

Hi there! I’m not able to reproduce you’re error on our system here to double-check.
So, I’m not sure whether it could be something related to Singularity (which we don’t use here) or maybe the version of PhyloPhlAn you’re using.

Can you provide the full command line of phylophlan_assign_sgbs and its version from

phylophlan_assign_sgbs --version

?

Thanks!

This is my version:

phylophlan_assign_sgbs.py version 3.0.40 (5 February 2024)

and also I receive this message:

sh: phylophlan_metagenomic: command not found

thank you

Lisa