KatharinaSchmid
commented
3 months ago Hey, thanks for your interest in our tool. We (and also other users) noticed that the GC correction can be quite slow on larger datasets. So your problem is very likely not an error, just a runtime problem. We are currently working on a faster approximation for the GC correction that can be used as an alternative. The new version is already implemented, we are just running some more tests to verify that the performance is still good enough with the alternative GC correction. In general, it is necessary to give epiAneufinder enough resources. On our compute cluster, a dataset with 3,000 cells runs in about 22h with 4 cores and 64GB of RAM per core. So I would suggest to first try and increase the resources, if this is possible for you. And I will let you know once we updated epiAneufinder with a faster GC correction. I hope this is helping you a bit. Best, Katharina
Hello! I have installed the tool and called it (it states that there are 32 warnings) However, it seems to be loaded just fine. when I run it on the sample, the first part is done and the .rds file is generated but then it gets stuck at the "correcting for GC bias", and there's no error, just as shown in the photo. it would be truly appreciated if you could help me with this, and tell me where the problem is. Thanks in advance! For your reference, this is my input data: https://cf.10xgenomics.com/samples/cell-arc/1.0.0/human_brain_3k/human_brain_3k_atac_fragments.tsv.gz