Reverse forward reads as input in MetaPhlAn 4

Microbial community profiling MetaPhlAn
1

Hi,

When I tried to run MetaPhlAn (v4.2.4) using flag -1 and -2 for the pair end reads, it gave me this error.

[Error] You specified forward and reverse reads, but did not specify --subsampling_paired. Provide the input as standard input or with -inp if you don’t want to subsample the reads with --subsampling_paired

What should I do because I not want to subsample the reads, but I am not sure what -inp does because -inp is not a flag? I appreciate any insight on this.

Many thanks,

2

Hi,

Did you find a workaround for this? I have also had the same error :slight_smile:

3

Hi,
MetaPhlAn does not use paired information except for when using the --subsampling_paired flag. If you do not want to subsample and have paired end reads you just give the reads as input as

metaphlan reads_R1.fq,reads_R2.fq …

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