Hi – I’m running MetaPhlAn4 V4.04 as follows:
metaphlan “${read1}”,“${read2}” --input_type fastq -o “${samplename}”_metaphlan --nproc 12 --bowtie2db /databases/metaphlan4_20230119/ --bowtie2out “${samplename}”_bowtie2out
The database in the specific folder is the contents of: mpa_vOct22_CHOCOPhlAnSGB_202212_bt2
I’m running it on a cluster with sbatch, so I don’t have the ability to provide user-input real-time.
The goal is to reproduce prior work that used that database, however MetaPhlAn provides a Y/N question asking if I want to download a new db, breaking the script. For this use case, I do not want to use the most recent datdabase, because I am trying to match a previously created dataset.
I have attempted to add the --offline flag, but that yields this error:
“Database cannot be downloaded with the --offline option activated”
I would really like to just be able to align to the mpa_vOct22_CHOCOPhlAnSGB_202212_bt2 database and, ideally, turn off any kind of auto-updating behavior permanently. Can you advise what the error is here and how to move forward?