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finalize README
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martin authored and martin committed Apr 7, 2023
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Expand Up @@ -137,7 +137,7 @@ Docker installation details [here](https://docs.docker.com/v17.09/engine/install

# Runtime and disk space

**Attention:** RIBAP is currently not intended to be used with hundreds or thousands of input genomes (see also [Limitations](#limitations)). Also for smaller input sets, you will need quite some disk space to store the ILPs and their results. Due to that, RIBAP is per default not storing the intermediate ILP files and solutions. You can use `--keepILPs` to store them, if needed. Below, we report runtime and disk space usage on a regular Linux laptop (8 CPUs used) and a HPC (SLURM, pre-configured CPU and RAM usage, runtime may be biased due to HPC work load) using varying numbers of _Chlamydia psittaci_ genomes (~1 Mbp, sampled from [here](https://osf.io/rbca9/)) as input and with and without the `--keepILPs` option. Please also not that we used the default `--chunks 8` value. Especially on a HPC, the runtime can be increased drastically by increasing the `--chunks` value.
**Attention:** RIBAP is currently not intended to be used with hundreds or thousands of input genomes (see also [Limitations](#limitations)). Also for smaller input sets, you will need quite some disk space to store the ILPs and their results. Due to that, RIBAP is per default not storing the intermediate ILP files and solutions. You can use `--keepILPs` to store them, if needed. Below, we report runtime and disk space usage on a regular Linux laptop (8 CPUs used) and a HPC (SLURM, pre-configured CPU and RAM usage, runtime may be biased due to HPC work load) using varying numbers of _Chlamydia psittaci_ genomes (~1 Mbp, originally sampled from [here](https://osf.io/rbca9/) and also available [here](https://osf.io/g52rb/)) as input and with and without the `--keepILPs` option. Please also not that we used the default `--chunks 8` value for local and HPC execution. Especially on a HPC, the runtime can be increased drastically by increasing the `--chunks` value (more parallel ILP solving).

| CPUs | #genomes (1 Mbp) | `--keepILPs` | time | `work` space | `output` space |
| ----------- | ----------- | ----------- | ----------- | ----------- | ----------- |
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