Ben J Woodcroft

Hmm, good question. My feeling is that it might be an issue where contig mode should be failing, but isn't. Hard for me to tell until I get to a...

Hi @nvpatin that seems like a completely different issue. Maybe ran out of RAM? Can you please check and if not can you post another issue with more details ie...

Hi, I can't remember actually, what files are kept that you would like to see deleted? Maybe the shortest path to a solution for you is to specify TMPDIR -...

Hi, Apologies for the slow response here. CoverM does not treat paired reads differently to how it treats single-ended reads. So if each read from a pair map to a...

Hi, Sorry I'm a bit lost. I think not everything you are saying there is quite correct, but what is your question/issue? -\------------- Ben Woodcroft Group leader, Centre for Microbiome...

The total mean coverage is just the sum of each genomes' mean coverage. The realative abundance is first calculated by working out the fraction of reads that map, and then...

No, because there's no need I don't think. Mean cov is the average number of reads covering a base in the genome, so in a sense that is already taken...

Right, though of course 1bp and 10bp are too short to actually map. But that aside, I agree. -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT ________________________________ From:...

Hi, From the timestamps it seems minimap2 finishes instantly, which isn't a good sign. Is something wrong with the input files or minimap2 executable?

Hi, What version is this? -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT ________________________________ From: Sabrin2020 ***@***.***> Sent: Thursday, August 31, 2023 2:03:44 AM To: wwood/CoverM ***@***.***> Cc:...