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# blastp_on_cluster | |
Script to run the BLAST step included in OrthoFinder on a cluster (OGE) | |
**NOTE: as OrthoFinder now supports DIAMOND, which is thousands of times faster than blast, this script is obsolete. Use a more recent version of OrthoFinder or enable sequence similarity searches using DIAMOND to reduce the runtime !** | |
## How it works | |
You need to run OrthoFinder using the **-op** option, to **only prepare** the blast files. At the end OrthoFinder will print the required blastp commands to the screen. This script will catch those commands and submit them as individual jobs (multi-threaded). | |
As such the clusters scheduler and queue is used, which is much more efficient than the one included in OrthoFinder. Also this allows the BLAST to run on multiple machines simultaniously. | |
## Usage | |
orthofinder.py -f <FASTA_DIR> -op | python3 blast_on_cluster.py | |
Once the cluster is done performing all the BLASTs your should resume OrthoFinder using the command below | |
orthofinder.py -b <BLAST_DIR> | |
## Todo | |
* Replace hard-coded stuff (like name of the blast module and number of threads) with arguments |