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  • Missing format options in standalone BLAST

    Hi,

    I am using latest version of standalone BLAST on linux. I tried to use custom output format and few options are missing. For example, I want to print the title of the subject along with the query, so I say

    -outfmt '6 qseqid stitle'

    With the above command I just get a list of queries. I tried to look at the available -outfmt options using blastn -help and I cant find stitle or salltitle options.

    Please help!

  • #2
    I used -outfmt "6 qacc sacc stitle score length mismatch gaps evalue qlen slen qstart qend sstart send" and in the third column I got the subject title. stitle is the correct option. Can you show the first five lines of the output file ?

    Comment


    • #3
      Hi,

      Here are the commands I used and the first five lines of the output,

      blastn -query /home/viraja/Desktop/samples_with_no_flags/sample_01/contigs_01_without_flag.fasta -db refseq -num_alignments 1 -outfmt '6 qseqid stitle'

      NODE_1_length_10131_cov_55.7043_ID_695104
      NODE_2_length_3299_cov_8.97446_ID_698840
      NODE_3_length_2648_cov_1.88378_ID_694314
      NODE_4_length_1757_cov_30.9221_ID_695832
      NODE_6_length_1496_cov_25.8736_ID_702132

      Comment


      • #4
        Originally posted by vpi View Post
        Hi,

        Here are the commands I used and the first five lines of the output,

        blastn -query /home/viraja/Desktop/samples_with_no_flags/sample_01/contigs_01_without_flag.fasta -db refseq -num_alignments 1 -outfmt '6 qseqid stitle'

        NODE_1_length_10131_cov_55.7043_ID_695104
        NODE_2_length_3299_cov_8.97446_ID_698840
        NODE_3_length_2648_cov_1.88378_ID_694314
        NODE_4_length_1757_cov_30.9221_ID_695832
        NODE_6_length_1496_cov_25.8736_ID_702132
        -num_alignments is not a valid flag for outfmt 6

        Also, are you sure you have setup refseq properly? Try with using full path to it..
        savetherhino.org

        Comment


        • #5
          Even without -num_alignments I get the same results. But earlier I tried num_alignments 1 -outfmt 6 and it worked.

          NODE_1_length_10131_cov_55.7043_ID_695104 gi|296556485|gb|M19921.2|HIVNL43 100.00 822 0 0 6686 7507 12281 11460 0.0 1519
          NODE_2_length_3299_cov_8.97446_ID_698840 gi|109255272|ref|NC_008168.1| 92.63 95 2 3 957 1051 25902 25991 2e-27 132
          NODE_3_length_2648_cov_1.88378_ID_694314 gi|237784637|ref|NC_012704.1| 82.29 2688 371 89 1 2648 114906 117528 0.0 2230
          NODE_4_length_1757_cov_30.9221_ID_695832 gi|154149549|ref|NC_009712.1| 78.86 175 33 4 490 663 2250989 2251160 1e-22 115
          NODE_6_length_1496_cov_25.8736_ID_702132 gi|304313778|ref|NC_014408.1| 76.42 246 45 9 666 903 324067 324307 2e-24 121
          NODE_7_length_1489_cov_0.428047_ID_692868 gi|170745058|ref|NC_010510.1| 95.06 1337 47 14 1 1325 547100 545771 0.0 2085

          If the path for refseq was not correct then the blast wouldn't run. Isnt it like that? Anyways I get the same result with full path as well (just query).

          Comment


          • #6
            What about -outfmt '6 std stitle' or -outfmt '6 std salltitles'. Perhaps refseq entries simply don't have subject titles? How did you create your refseq? Did you download it from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and simply tar zxvf?
            Last edited by rhinoceros; 10-18-2013, 02:54 AM.
            savetherhino.org

            Comment


            • #7
              You said 'latest', but which version of BLAST+ exactly are you using?

              Comment


              • #8
                Originally posted by vpi View Post
                Hi,

                I tried to look at the available -outfmt options using blastn -help and I cant find stitle or salltitle options.

                Please help!
                This bit of information ties directly to maubp's question. Which version are you using? Run this command to find out.

                Code:
                # blastn -version
                The stitle & salltitle outfmt options were only added in the latest version, 2.2.28 (released April 2013). If you don't see them listed in the help message then it is a good guess that you don't really have the latest version.

                Comment


                • #9
                  -outfmt '6 std stitle' gives the same output as -outfmt 6

                  I downloaded this latest version for linux ncbi-blast-2.2.28+-x64-linux.tar.gz. But when I run the command blastn -version, it says BLAST 2.2.27+. This might be the problem. What might be wrong?

                  Comment


                  • #10
                    Originally posted by vpi View Post
                    -outfmt '6 std stitle' gives the same output as -outfmt 6

                    I downloaded this latest version for linux ncbi-blast-2.2.28+-x64-linux.tar.gz. But when I run the command blastn -version, it says BLAST 2.2.27+. This might be the problem. What might be wrong?
                    Did you install 2.2.28+ properly after downloading? Did you remove 2.2.27+? Or are both versions installed and is 2.2.27+ taking precedence based on their order in your $PATH environment variable?

                    Comment


                    • #11
                      I never installed 2.2.27+ at all. The first time I installed is BLAST 2.2.28+.

                      Comment


                      • #12
                        Originally posted by vpi View Post
                        I never installed 2.2.27+ at all. The first time I installed is BLAST 2.2.28+.
                        Well the output from "blastn -version" sort of disputes that statement doesn't it? Could someone else have installed 2.2.27?

                        Comment


                        • #13
                          Someone installed 2.2.27+, so what do these give:
                          Code:
                          which blastn
                          and:
                          Code:
                          echo $PATH

                          Comment


                          • #14
                            I totally agree with you kmcarr. Its very confusing for me too. I got a brand new computer and I installed everything myself. So I know whats on the computer.

                            which blastn
                            /usr/bin/blastn

                            echo $PATH
                            /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/viraja

                            Comment


                            • #15
                              Originally posted by vpi View Post
                              -outfmt '6 std stitle' gives the same output as -outfmt 6

                              I downloaded this latest version for linux ncbi-blast-2.2.28+-x64-linux.tar.gz. But when I run the command blastn -version, it says BLAST 2.2.27+. This might be the problem. What might be wrong?
                              2.2.27 is in your path where as 2.2.28 is not or has lesser 'priority'. You can override this by running blast 2.2.28 from the folder where you installed it by ./blastn .. or by specifying the path to it, or by removing 2.2.27.
                              savetherhino.org

                              Comment

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