Hi, I am using MetaPhlAn version 3.0.14, in the help, the gzip file format is not mentioned. May I ask whether the gzip fastq can be directly used as input for MetaPhlAn? If so, the --input_type should be selected “fastq”? For example, the part of command as below:
metaphlan xxx_1.fastq.gz,xxx_2.fastq.gz --input_type fastq
When running successfully, there is “WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.
An additional column listing the merged species is added to the MetaPhlAn output.” for some samples, may I ask whether this is normal, and can be ignored or what to do?
Thanks
Wang