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  • kmcarr
    replied
    Originally posted by vpi View Post
    Thank you so much. Everything works fine now. But I have a new issue.

    The blast output file has repeated results, I mean the query, subject is repeated several times, even though I use -num_alignments 1. For example,

    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    '-num_alignments' only applies to output formats which actually include alignments (e.g. outfmt 0,1,2,3,4); it is meaningless (and therefore ignored) for tabular output formats like yours.

    Parameters which limit the number of reported hits in tabular output are -max_target_seqs and -max_hsps_per_subject.

    But you should be aware that by limiting the number of alignments reported for each query you may be throwing away important data. What the output you have shown above indicates is that this particular query (NODE_20) aligns to multiple locations on the genome of Desulfitobacterium hafniense DCB-2. That may be important!

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by vpi View Post
    Thank you so much. Everything works fine now. But I have a new issue.

    The blast output file has repeated results, I mean the query, subject is repeated several times, even though I use -num_alignments 1. For example,

    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    As I wrote earlier, -num_alignments (Show alignments for this number of database sequences) is an invalid flag for outfmt 6 since it doesn't show any alignments to begin with. There are other flags that you could try in the blast manual. This thread is also highly relevant.

    Leave a comment:


  • vpi
    replied
    Thank you so much. Everything works fine now. But I have a new issue.

    The blast output file has repeated results, I mean the query, subject is repeated several times, even though I use -num_alignments 1. For example,

    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52
    NODE_20_length_864_cov_1.18725_ID_1126030 gi|219666071|ref|NC_011830.1| Desulfitobacterium hafniense DCB-2, complete genome 2e-52

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by vpi View Post
    Could you please explain how can I delete them. I tried to delete them directly from the folder but I failed.
    Code:
    rm /usr/bin/blastn
    Removes the blastn binary. If it says something about rights then:

    Code:
    sudo rm /usr/bin/blastn
    There will probably still be other blast 2.2.27+ related binaries in your "/usr/bin". If you installed it by apt-get, this describes how to remove it.

    Leave a comment:


  • vpi
    replied
    Could you please explain how can I delete them. I tried to delete them directly from the folder but I failed.

    Leave a comment:


  • rhinoceros
    replied
    Like kmcarr said except instead of rearranging $PATH you could just delete the blast 2.2.27+ binaries from "/usr/bin".

    Leave a comment:


  • kmcarr
    replied
    Originally posted by vpi View Post
    Both of you were correct.

    Now after chnaging the path,

    echo $PATH
    /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/me/ncbi-blast-2.2.28+/bin


    blastn -version
    blastn: 2.2.27+
    Package: blast 2.2.27, build Oct 29 2012 07:36:27

    But still says blast 2.2.27+
    Because "/usr/bin" which is where 2.2.27+ is located, comes BEFORE "/home/me/ncbi-blast-2.2.28+/bin" in your $PATH variable.

    When you have more than one copy of program installed, *NIX systems choose the one which comes FIRST in your $PATH. You have to rearrange the order of directories in your $PATH.

    Leave a comment:


  • vpi
    replied
    Both of you were correct.

    Now after chnaging the path,

    echo $PATH
    /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/me/ncbi-blast-2.2.28+/bin


    blastn -version
    blastn: 2.2.27+
    Package: blast 2.2.27, build Oct 29 2012 07:36:27

    But still says blast 2.2.27+

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by vpi View Post
    I downloaded it to the downloads folder, but then I moved it to home directcory and decompressed it there.
    The general way to put things into your path is to add them to .bashrc or .bash_profile (or whatever your distro has). In terminal type

    cd

    and then

    ls -la

    and you'll see some file like this. Next edit it with for example nano, i.e.

    nano .bashrc

    and add the path there, e.g.

    export PATH=/Users/you/Software/ncbi-blast-2.2.28+/bin:${PATH}

    Next

    source .bashrc

    and if you added the correct bin directory (what you see when you type pwd in the blast dir), it's now in your path. It's sort of like creating shortcuts in Windows.
    Last edited by rhinoceros; 10-18-2013, 08:09 AM.

    Leave a comment:


  • vpi
    replied
    I downloaded it to the downloads folder, but then I moved it to home directcory and decompressed it there.

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by vpi View Post
    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.
    I bet you downloaded and uncompressed blast 2.2.28 and then left it at that (didn't put it into your path), went to the terminal and typed blastn and then your distro pulled blast 2.2.27 from some repo in which the latest blast is 2.2.27.

    Leave a comment:


  • maubp
    replied
    This version looks for the first copy of 'blastn' in the list of folders defined with $PATH,

    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'

    By specifying the path to BLAST 2.2.28+, you tell Linux exactly where to look. We mean sdo omething like this, where I'm assuming you downloaded and decompressed the BLAST 2.2.28+ files under /home/viraja/downloads/ - adjust to match your setup:

    /home/viraja/downloads/ncbi-blast-2.2.28+/bin/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'
    Last edited by maubp; 10-18-2013, 07:51 AM. Reason: typo

    Leave a comment:


  • rhinoceros
    replied
    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.

    Leave a comment:


  • vpi
    replied
    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

    Leave a comment:


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

    Leave a comment:

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