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Running psiblast on AWS with ElasticBlast

Hi all, I'm trying to run a psiblast query using elasticblast on aws. I have a .ini file setup with correct paths, however I want to save the pssm matrix after the last iteration, so I set the -save_pssm_after_last_round in the [blast] options setting. My question is how to save the pssm using -out_ascii_pssm such that all my pssm files don't overwrite each other. Is there a programmatic solution to this? I'm using a single fasta file with ~300 sequences on an s3 bucket, should I split these into individual files?

Thanks in advance

psiblast blast

1 answer

If you need a per sequence PSSM file then you will need to run these as individual jobs specifying a new output file for -out_ascii_pssm file_name.mat.

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