run_all.py taking forever

[nitinra]

Hello,

I am running swiftortho for 276 insect species. I used the following command

python run_all.py -i allprotein.fa -a 20

I started the run on Jan 30th and it's still running the first step (all-vs-all homology search). Is there anyway I can make it run faster?

Regards,
Nitin

[Rinoahu]

How many protein sequences are in the file? Are they the same species?

[nitinra]

Hello,

The insects species span across the entire insect clade, so 276 different species and the # of sequences in my fasta file is ~6839337 sequences (in the combined fasta file).

How do I make it run faster? thank you!

Regards,
Nitin

[Rinoahu]

1. delete the old version

2. git clone the latest one

3. install according to the instructions

4. Run the command:
   python run_all.py -i allprotein.fa -a 20 -s 11111111 -v 500

5. You can also try the new tool if the protein sequences have a lot of redundancy
   python run_all_fast.py -i allprotein.fa -a 20 -s 11111111 -v 500

Generally, increasing the seed length or reducing the number of hit at homolog search can make it run faster