Blast error for rosetta antibody: No argument value given for Query file

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    • June 9, 2021 at 12:30 am #3782
      Anonymous

        Hi there,

         When I try to run rosetta antibody with,

        “antibody.linuxgccrelease -fasta mAb2.fasta | tee grafting.log”

        I encounter error message ” ERROR: basic.execute encounter error while runnning blastp [-db, /home/user/rosetta/rosetta3.13/main/database/additional_protocol_data/antibody//blast_database/database.FRH, -query, grafting/frh.fasta, -out, grafting/frh.align, -word_size, 2, -outfmt, 7, -max_target_seqs, 1024, -evalue, 0.00001, -matrix, BLOSUM62]

         How can I solve it?

        Thanks

      • June 9, 2021 at 11:38 pm #15917
        Anonymous

          I see that your title contained relevant information that I missed the first time. My previous response is no good.

          It looks like the  “frh.fasta” is not being crated. Would you be willing to share your fasta file? are the labels in it correct? Heavy chain’s description should be “heavy”. Do the framework regions match what you would expect? What organism did it come from? Is it a complete variable region or does the sequence start after framework1? 

          Previous response:

          Guessing you don’t have blastp installed. This link says you need at least version 2.2: https://new.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol

          Here is the link to the directory on the nih ftp server where you can find the download the latest version: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

          If that does not work downgrade to version 2.2

          I would just use the tar. You will likely need to add the line:

          ”’

          export PATH=”YOUR_BLAST_PATH_HERE:$PATH”

          ”’

          to your .bashrc / .zshrc / whatever

          Please let me know if additional clarification would be helpful.

           

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