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  • File not found on running blastall?

    blastall -p blastn -d sample1_Assembly -i seq.fa -F F

    Always have the issue of this as following:

    Exception(FILE): sample1_Assembly.nbl: No such file or directory
    I used the formatdb to generate the blastdb. It generate 5 files:
    sample1_Assembly.nhr
    sample1_Assembly.nin
    sample1_Assembly.nsd
    sample1_Assembly.nsi
    sample1_Assembly.nsq
    Any thoughts on this?

  • #2
    You appear to be running an old version of blast (since you are using blastall). Is there a specific reason for that and what version are you using?

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    • #3
      Originally posted by GenoMax View Post
      You appear to be running an old version of blast (since you are using blastall). Is there a specific reason for that and what version are you using?
      Thanks for your reply. It is just as installed on the server. Do not have the privilege to update it. Any other ways, using an old version of formatdb?

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      • #4
        You should be able to use a newer version from your own directory. You can find the source (as well as pre-compiled executables) here: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/LATEST/

        What command line options did you use for formatdb?

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        • #5
          Originally posted by GenoMax View Post
          You should be able to use a newer version from your own directory. You can find the source (as well as pre-compiled executables) here: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/LATEST/

          What command line options did you use for formatdb?
          Sorry to reply late.

          formatdb -i “input file” -p F -n “Name of db” -o T -l “log file”

          but it just cannot generate the *.nbl file. Thanks in advance.

          Comment


          • #6
            Originally posted by GenoMax View Post
            You should be able to use a newer version from your own directory. You can find the source (as well as pre-compiled executables) here: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/LATEST/

            What command line options did you use for formatdb?
            The thing is I have some other old blastdb databases at the moment. So if I have to use the new version of the blast, all the old bast database have to be modified. Too costly. : |

            Comment


            • #7
              Originally posted by arkilis View Post
              The thing is I have some other old blastdb databases at the moment. So if I have to use the new version of the blast, all the old bast database have to be modified. Too costly. : |
              It seems to me that you would only have to use the new blast on the one database giving you problems -- sample1_Assembly. Your other databases could be left alone.

              Granted there is a learning curve for the new Blast. The command line switches are different. However support is almost always better for a current program, especially since the new version of Blast has been out for several years by now.

              As to your question. I've never seen the *.nbl file before thus am unsure what it is used for. Your formatdb and blastall commands seem to be fine.

              Comment

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