Hi, I’m using metaphlan 2 in Galaxy (Europe) to analyze microbiome data from the a fastqsanger file from paired end sequencing that I downloaded from Qiita and ENA Browser. I can’t seem to run the file and keep getting an error that says that the fastqsanger format is not supported. I then use a FASTQ to FASTA tool in Galaxy which is then able to run Metaphlan2 but I keep getting “unclassified” in the community profile output. I’m using sequence data from just one of the reads (R1). I’ve tried this with other sequences from other metagenomic studies but I keep receiving “unclassfied” as the output. What am I doing wrong?
HI @Pouria
Unfortunatelly, metaphlan 2 is not currently supported, I would suggest you to update to version 3 or even to the latest version 4