Commit d61c2a8c authored by Sam Nooij's avatar Sam Nooij
Browse files

Add note on --keep-going when pyANI might fail

parent 767dde15
......@@ -104,7 +104,12 @@ species:
- Norovirus
```
_Note that genus names also work._
_Note that genus names also work._
_Also note that the scaffolds of the species of interest will be compared to one another with [pyANI](https://pypi.org/project/pyani)._
_This will only work when there is enough sequence overlap, so usually if the species is sufficiently abundant._
_When using species that are not expected to be highly abundant, the pipeline is likely to return an error._
_To ignore this and continue with all other steps, add the parameter `--keep-going` can be used with your snakemake command._
_(See [below](2-running-the-pipeline) for an example.)_
#### Make sure you have snakemake installed
......@@ -137,7 +142,12 @@ And when that works fine, the pipeline may be started:
snakemake -p -j 8 --use-conda
```
On a local system (if necessary, change the '8' for the appropriate number of CPU threads on your system).
On a local system (if necessary, change the '8' for the appropriate number of CPU threads on your system).
When a species with a low expected abundance is selected, please consider using `--keep-going` to ignore possible errors in the comparison of scaffolds:
```bash
snakemake -p -j 8 --use-conda --keep-going
```
If you are working on an HPC cluster, you may use commands like:
......
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