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Script to run the BLAST step included in OrthoFinder on a cluster (OGE)
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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NOTE: as OrthoFinder now supports DIAMOND, which is thousands of times faster than blast, this script is obsolete.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 -f <FASTA_DIR> -op | python3

Once the cluster is done performing all the BLASTs your should resume OrthoFinder using the command below -b <BLAST_DIR>


  • Replace hard-coded stuff (like name of the blast module and number of threads) with arguments
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