keep getting error with psiblast

keep getting error with psiblast

1

hello

I am trying to calculate the PSSM but I keep getting error , where is the problem in this code ?

import os
import re

def command_pssm(content, output_file,pssm_file):

    os.system('psiblast 
              -in_msa 1ak4.fasta 
              -db allseq.fasta 
              -num_threads 10 
              -num_iterations 3 
              -evalue 0.001 
              -out output_file
              -out_ascii_pssm PSSM.txt' )

input_file = "1ak4.fasta"
output_file = "myoutput.txt"
out_ascii_pssm ="PSSM.txt"

command_pssm(input_file, output_file, out_ascii_pssm)

as an example I get the following error

BLAST query error: CAlnReader::GetSeqEntry(): Seq_entry is not available until after Read()

even when I run this command, I get the same error

psiblast -subject 1ak4.fasta -in_msa allseq.fasta -out_ascii_pssm pssm.txt
BLAST query error: CAlnReader::GetSeqEntry(): Seq_entry is not available until after Read()


psiblast


python


blast

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