Ka Ming Nip
Ka Ming Nip
No, there is no feature for specifying read depth because that kind of information is not tracked during simulation.
Can you please report the exact command? And are you using the code from the master branch?
As a test, you could try taking out these options: `--abun_var -0.5 0.5` and `--max_len 1700`
> if I specify --max_len of 100 less than the minimum genome length it never gets stuck in an infinite loop. This worked because the ~100 nt buffer accounted for...
Hi @danpal96, @ahfitzpa , @aastha-batta , and @rameezmj I have created pull request #189. Can you please check whether my changes would resolve the hanging issues on your end?
@danpal96 No worries, we appreciate your help!
> ValueError: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 1 is required. Can you please report your exact command and your TSV file for `--genome_list`? >...
The existing models in NanoSim are very old. If you have an ONT dataset with the right basecaller+chemistry combination, then you can subsample to 1 million reads and run the...
That's an interesting proposition; I think it can be done. First, you will need to simulate a set of reads (with `simulator.py`). Note that each simulated read has the corresponding...
I think it has to do with these settings: `-n 20000 -max 10000 -min 200` It sounds like a similar issue in metagenome mode: https://github.com/bcgsc/NanoSim/issues/184 @SaberHQ Possibly a bug in...