Additional Benchmarking to be added to README? #285
Description
/hot/user/sfitzgibbon/PCAWG-63/benchmark-call-ssnv
Input was 30 tumor/normal pairs from the PCAWG-63 dataset, chosen because they had complete pipeline-call-sSNV results. Default v8.0.0 F72.config resources were used.
Sample IDs:
/hot/user/sfitzgibbon/PCAWG-63/benchmark-call-ssnv/benchmark-30-tumor.txt/hot/user/sfitzgibbon/PCAWG-63/benchmark-call-ssnv/benchmark-30-normal.txt
Nextflow trace files:
/hot/user/sfitzgibbon/PCAWG-63/benchmark-call-ssnv/PCAWG-trace-files
Per sample mean coverage:
/hot/user/sfitzgibbon/PCAWG-63/benchmark-call-ssnv/benchmark-30-tumor-meanCoverage.txt/hot/user/sfitzgibbon/PCAWG-63/call-ssnv-benchmark/benchmark-30-normal-meanCoverage.txt
Sample coverage
| type | min | max | average |
|---|---|---|---|
| tumor | 24x | 71x | 44x |
| normal | 24x | 50x | 32x |
Runtimes per sample (summed over parallel jobs)
| Tool | min | max | average |
|---|---|---|---|
| MuSe | 1h 54m | 4h 40m | 3h 6m |
| Mutect2 | 68h 10m | ||
| SomaticSniper | 13h 15m | ||
| Strelka2 | 5h 30m |
Cpus per sample
| Tool | min | max | average |
|---|---|---|---|
| MuSe | 1174% | 1191% | 1185% |
| Mutect2 | 4733% | ||
| SomaticSniper | 291% | ||
| Strelka2 | 1121% |
CPUhours
| Tool | average |
|---|---|
| MuSe | |
| Mutect2 | |
| SomaticSniper | |
| Strelka2 |
Memory (max rss)
| Tool | min | max | average |
|---|---|---|---|
| MuSe | 33.3 GB | 46.8 GB | 39.1 GB |
| Mutect2 | 27.7 GB | ||
| SomaticSniper | 4.41 GB | ||
| Strelka2 | 3.32 GB |