I am using biobakery_workflows v3.0.0-alpha.7. I am trying to obtain taxonomic profiling in absolute reads (mapped or from total reads).
I ran this code:
biobakery_workflows wmgx
–input-extension fastq.gz
-o /media/AD/
–threads 6
–local-jobs 2
–remove-intermediate-output
–bypass-strain-profiling
–bypass-functional-profiling
–taxonomic-profiling-options=“–add_viruses -t marker_counts”
The output file does not change.
I tried running just metaphlan using sam input
metaphlan --input_type sam
-t marker_counts
–nproc 4
-o /media/AD/metaphlan_marker_counts/
I received this message
Please provide the size of the metagenome using the --nreads parameter when running MetaPhlAn using SAM files as input. Exiting