Sample2markers don't generate any pkl files, but instead generate json.bz2 files

Microbial community profiling StrainPhlAn
1

I am going to strainphlan4 to abtain strain level data from mgs data, but when I use command sample2markers.py -i sams/*.sam.bz2 -o consensus_markers -n 8, I don’t get any pkl files, but json.bz2 files. I don’t know how to solve this problem, please help me, thanks
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2

I have solved. In strainphlan4.1 version, the json files replace pkl files.

1 Like
3

So how did you solved it? Do you use a older version of strainphlan or metaphlan?

4

Hi, this is not an issue. Since StrainPhlAn 4.1, the output of sample2markers is in JSON format (not .pkl anymore), as described in the changelog of MetaPhlAn 4.1. The only difference is that now you will provide JSON files during the strainphlan command execution instead of .pkl.

5

Hi, I am facing the same situation but with biobakery_workflow wmgx. The workflow expects a pkl file not a json.bz2. Do you know how I can modify the workflow in order to change the expected extension?
Thanks

6

Hi there, I’ve managed to solve it by replacing:
1 biobakery_workflows/utilities.py
2 biobakery_workflows/tasks/shotgun.py

More details here: Add strainphlan wildcard in one more location · biobakery/biobakery_workflows@c9a6adb · GitHub

Best regards