I’m running into a problem using the biobakery wmgx pipeline to run metaphlan (v4.0.6) and humann (v3.6).
I initially ran the pipeline to perform only kneaddata and metaphlan taxonomic profiling (with --bypass-functional-profiling). I later decided I wanted to run the functional profiling so I used the same command, removing ‘–bypass-functional-profiling.’ The pipeline successfully skips kneaddata steps, but begins re-running the taxonomic profiling with metaphlan.
If I use --bypas-taxonomic-profiling the pipeline does not work, as the input folder is then the original fastq files (not taxonomic profiles). It gives the error “ERROR: Bypassing taxonomic profiling but all of the tsv taxonomy profile files are not found in the input folder. Expecting the following input files:”
However, changing the input folder to the location of the metaphlan-generated tsv taxonomic profiles gives the error “ERROR: No files were found in the folder with extension fastq.gz”
Is it possible to continue with the pipeline from this point without re-running metaphlan? I know I could run humann on the files without the pipeline, but it’s convenient to run this way with the slurm scheduling, as I have many files.
Thanks for the support!