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
Thank you Lisa and apologies for the late reply.
So, in the latest PhyloPhlAn release phylophlan_metagenomic was renamed phylophlan_assign_sgbs. I suspect that updating the code to the latest version will solve this. If you install PhyloPhlAn version 3.1 (this is the version of the package in bioconda), you should then see this from the console:
$ phylophlan_assign_sgbs --version
phylophlan_assign_sgbs.py version 3.1.40 (6 March 2024)
Can you try this update and let me know if you are able to solve this?
Many thanks,
Francesco