Abundance calculation about genome

[maocheng2020]

Hi，When I run with the following command, coverm genome --coupled AR1.fastq AR2.fastq B_R1.fastq B_R2.fastq C_R1.fastq C_R2.fastq D_R1.fastq D_R2.fastq E_R1.fastq E_R2.fastq F_R1.fastq F_R2.fastq \ --genome-fasta-directory bin \ -o output.tsv \ --min-read-percent-identity 0.95 --min-read-aligned-percent 0.75 --trim-min 0.10 --trim-max 0.90 --threads 6

I got, In sample 'AR1.fastq', found 6036415 reads mapped out of 138369022 total (4.36%), In sample 'BR1.fastq', found 6368243 reads mapped out of 142599600 total (4.47%)......

and the output.tsv ,I found no information about *R2.fastq',I expected the result to be the abundance of the sample A instead of sample A_R1.fastq. Sorry to bother you，thanks.

[rhysnewell]

Hi! This is standard behaviour, CoverM just uses the forward read filename as a proxy for the sample name as whole. It's definitely mapping both forward and reverse reads.

Cheers, Rhys

[Sabrin2020]

I tried to update , I uninstalled and reinstalled from here https://anaconda.org/bioconda/coverm but ended up with same version. How can I install latest version with conda please?