I’m using biobakery workflows for years. I I always used lastest database, but in this case I decided to keep using mpa_vOct22_CHOCOPhlAnSGB_202212 cause of analysis consitency inside an experiment. I ran code as usually:
biobakery_workflows wmgx --input-extension fastq.gz -o /Biobakery_Results/SER05 --threads 3 --local-jobs 2 --bypass-strain-profiling --remove-intermediate-output --qc-options=–bypass-trf
I realized that MetaPhlAn tasts started but didn’t go further for days. Then I tried to run MetaPhlAn separately and a message asked me if I would like to update database or use the previous one Yes/No?
I could fix it adding the taxonomic-profiling-option offline to the code_
biobakery_workflows wmgx --input-extension fastq.gz -o /Biobakery_Results/SER05 --threads 3 --local-jobs 2 --bypass-strain-profiling --remove-intermediate-output --qc-options=–bypass-trf --taxonomic-profiling-options=–offline
I hope my experience helps to other users.