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  • Genome Browser (for Synteny)

    Gateway Time-out

    The gateway did not receive a timely response from the upstream server or application.
    When I using the GBrowse synteny (gbrowse_syn), I got the error in above.
    How can I handle this error?

    Below is my database set. (test custom data)

    mysql> select * from map;
    +--------+----------+-------+------+------+
    | map_id | hit_name | src1 | pos1 | pos2 |
    +--------+----------+-------+------+------+
    | 1 | H000001 | cat | 1 | 60 |
    | 2 | H000001 | tiger | 50 | 10 |
    | 3 | H000002 | cat | 53 | 153 |
    | 4 | H000002 | tiger | 101 | 100 |
    | 5 | H000003 | cat | 90 | 180 |
    | 6 | H000003 | tiger | 100 | 10 |
    | 7 | H000004 | cat | 500 | 1803 |
    | 8 | H000004 | tiger | 1302 | 1000 |
    +--------+----------+-------+------+------+
    8 rows in set (0.00 sec)

    mysql> select * from alignments;
    +--------+----------+-------+------+--------+------+---------+------+--------------+-------+------+--------+------+---------+------+
    | hit_id | hit_name | src1 | ref1 | start1 | end1 | strand1 | seq1 | bin | src2 | ref2 | start2 | end2 | strand2 | seq2 |
    +--------+----------+-------+------+--------+------+---------+------+--------------+-------+------+--------+------+---------+------+
    | 1 | H000001 | cat | A1 | 1 | 10 | + | | 1000.000000 | tiger | 123 | 50 | 60 | - | |
    | 2 | H000001r | tiger | 123 | 50 | 60 | + | | 1000.000000 | cat | A1 | 1 | 10 | - | |
    | 3 | H000002 | cat | A1 | 53 | 100 | + | | 1000.000000 | tiger | 292 | 101 | 153 | + | |
    | 4 | H000002r | tiger | 292 | 101 | 153 | + | | 1000.000000 | cat | A1 | 53 | 100 | + | |
    | 5 | H000003 | cat | A1 | 90 | 10 | + | | 1000.000000 | tiger | 80 | 100 | 180 | + | |
    | 6 | H000003r | tiger | 80 | 100 | 180 | + | | 1000.000000 | cat | A1 | 90 | 10 | + | |
    | 7 | H000004 | cat | A1 | 500 | 1000 | + | | 10000.000000 | tiger | 202 | 1302 | 1803 | - | |
    | 8 | H000004r | tiger | 202 | 1302 | 1803 | + | | 1000.000001 | cat | A1 | 500 | 1000 | - | |
    +--------+----------+-------+------+--------+------+---------+------+--------------+-------+------+--------+------+---------+------+
    8 rows in set (0.00 sec)

  • #2
    The problem is your proxy latency, not the data.

    Comment


    • #3
      Originally posted by TiborNagy View Post
      The problem is your proxy latency, not the data.

      Thanks, for your reply. I'll try to change.

      Could you help me how I can change the proxy latency in linux server? Is it rely on the server configuration? or my computer?

      Comment


      • #4
        Originally posted by TiborNagy View Post
        The problem is your proxy latency, not the data.
        I miss one.

        When I tried to view the example data in GBrowse_syn package, it is works.
        (rice genome) but, with this custom data isn't works

        Comment


        • #5
          If the test data works then this may be a read permissions issue for the "www-data" user (or which ever user you are using) for your custom database.

          Comment


          • #6
            Originally posted by GenoMax View Post
            If the test data works then this may be a read permissions issue for the "www-data" user (or which ever user you are using) for your custom database.
            I tried it in above.
            But, as before I got the same error.
            Anyway, thanks for your comment.

            Comment


            • #7
              Please check your Apache server logs. (usually: /var/log/apache2/error.log)

              Comment

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