Michael Hall

Update: I think it may have something to do with the popup box that shows up when typing in the caption section.

I am seeing a similar issue with a reference fasta that is 1.1Gb and reads around 2Gb. However, I am not seeing the `[morecore] insufficient memory` error, I am just...

In my use case, the reference is a 16S rRNA database (sequences all around 1.5Kb) and the reads are also from 16S rRNA sequencing (reads have been filtered to 1.4-1.6Kb)....

> High memory usage is expected, given the repetitiveness of the reference data. Another example. I have a sample that is (compressed) 311MB in size, mapping to the database I...

> The repetitiveness is really high here. The peak memory will depend on what sequences are being mapped at the same time across threads. It can vary a lot. One...

> We're seeing something similar with one of our PhD students too. She's aligning a ~1.6 GB FASTQ to a set of 16S references (n=~21000, 50Mb). The job slowly but...

I was able to get 20/22 samples to complete within 100Gb RAM with the following options ```sh minimap2 -K 100M --no-kalloc --print-qname -aLx map-ont -t 1 ``` I am trying...

Ok, so to get my samples to all run in under 50Gb RAM I had to use the following options ```sh minimap2 -t 1 -K 25M --no-kalloc --print-qname -aLx map-ont...

It's not immediately obvious to me sorry. I won't be able to look at this until sometime late next week either sorry.

Hi @corneliusroemer The two spaces around configfile is a conscious decision we made along with @johanneskoester. Regarding configuration, the only real [configuration options](https://github.com/snakemake/snakefmt#configuration) are those in the CLI options, or...