From 1b55a6d6a3424d1f5b8c4463298eab30a64435f8 Mon Sep 17 00:00:00 2001 From: jvfe Date: Thu, 1 Feb 2024 09:17:07 -0300 Subject: [PATCH] docs(usage): Add note about storage requirements Signed-off-by: jvfe --- docs/usage.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 3ce71db..245b111 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -350,3 +350,11 @@ NXF_OPTS='-Xms1g -Xmx4g' Sometimes LevelDB, which is used by Nextflow to track execution metadata, can lead to memory-related issues, often showing as a **SIGBUS** error. [This tends to happen when running Nextflow in SLURM environments](https://github.com/nextflow-io/nextflow/issues/842). In this case, setting `NXF_OPTS="-Dleveldb.mmap=false"` in your `~/.bashrc` or immediately before executing `nextflow run` usually solves the issue. + +## ARETE's storage requirements + +ARETE generates a lot of intermediary files, which is even further exacerbated if you are running on a dataset with more than 100 genomes. +Before running ARETE you should make sure you have at least 500 GB of free storage. + +After running ARETE and checking your results, you can remove the `work/` directory in your working directory, which is where Nextflow stores its cache. +**Be aware that deleting `work/` will make it so your pipeline won't re-run with cache when using the `-resume` flag, it will run every process from scratch.**