Genome Browser (for Synteny)

[Hyunmin]

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)

[TiborNagy]

The problem is your proxy latency, not the data.

[Hyunmin]

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?

[Hyunmin]

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

[GenoMax]

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.

[Hyunmin]

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.

[TiborNagy]

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