Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

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Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Sheldon McKay
I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim


[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)

This is ok. (example data in GBrowse) http://www.hanjunghun.com/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:1563265..1659500

But, I can’t load the my example data. Below is error message after has an long loading time..

http://www.hanjunghun.com/cgi-bin/gb2/test_syn/syn_demo/
http://www.hanjunghun.com/cgi-bin/gb2/test_syn/syn_demo/?search_src=cat;name=A1:10313297..10663825

Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

------------------------------------------------------------------------------
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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oryza.synconf (1K) Download Attachment
=?utf-8?Q?rice=5Fsynteny.conf?= (670 bytes) Download Attachment
=?utf-8?Q?wild=5Frice=5Fsynteny.conf?= (916 bytes) Download Attachment
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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)

This is ok. (example data in GBrowse) http://www.hanjunghun.com/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:1563265..1659500

But, I can’t load the my example data. Below is error message after has an long loading time..

http://www.hanjunghun.com/cgi-bin/gb2/test_syn/syn_demo/
http://www.hanjunghun.com/cgi-bin/gb2/test_syn/syn_demo/?search_src=cat;name=A1:10313297..10663825

Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

------------------------------------------------------------------------------
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Sheldon McKay
For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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applications. Written by three acclaimed leaders in the field,
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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim
Thanks for your reply.

I attached my error log file.

 One is that there are no alignments in the browser

Maybe, it bacause of test data. (my mistake)

The second is that no annotations (from the GFF) are visible for wild rice.

same reason. I didn’t prepare annotation data not yet.

anyway, I’ll try to re-set the gbrowse (synteny) with real my data. and I’ll report it for you.

Thanks.


켜짐 2014년 3월 19일 at 오후 5:39:18, Sheldon McKay ([hidden email]) 작성됨:

For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech_______________________________________________
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------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-gbrowse mailing list
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=?utf-8?Q?syn.error=5Flog?= (8K) Download Attachment
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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim
http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=human;name=chr4:22729207..22729574

With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But,  remain unchanged

http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=human;name=chr4:22729207..22729574


켜짐 2014년 3월 25일 at 오후 4:53:17, Hyunmin Kim ([hidden email]) 작성됨:

Thanks for your reply.

I attached my error log file.

 One is that there are no alignments in the browser

Maybe, it bacause of test data. (my mistake)

The second is that no annotations (from the GFF) are visible for wild rice.

same reason. I didn’t prepare annotation data not yet.

anyway, I’ll try to re-set the gbrowse (synteny) with real my data. and I’ll report it for you.

Thanks.


켜짐 2014년 3월 19일 at 오후 5:39:18, Sheldon McKay ([hidden email]) 작성됨:

For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim

With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But, remain the same (no result) Why? 

please confirm it.

mysql> select * from alignments LIMIT 5;
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
| hit_id | hit_name     | src1   | ref1 | start1    | end1      | strand1 | seq1 | bin          | src2   | ref2 | start2    | end2      | strand2 | seq2 |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
|      1 | H0000000001  | hg19   | chr4 |  22729207 |  22729574 | +       |      |  1000.022729 | gallus | 4    |   2233797 |   2234164 | +       |      |
|      2 | H0000000001r | gallus | 4    |   2233797 |   2234164 | +       |      | 10000.000223 | hg19   | chr4 |  22729207 |  22729574 | +       |      |
|      3 | H0000000002  | hg19   | chr4 | 110268510 | 110268621 | +       |      |  1000.110268 | gallus | 4    |   4431008 |   4431119 | +       |      |
|      4 | H0000000002r | gallus | 4    |   4431008 |   4431119 | +       |      |  1000.004431 | hg19   | chr4 | 110268510 | 110268621 | +       |      |
|      5 | H0000000003  | hg19   | chr4 | 170616761 | 170616846 | +       |      |  1000.170616 | gallus | 4    |   9653424 |   9653509 | +       |      |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
5 rows in set (0.00 sec)

mysql> select * from map LIMIT 5;
+--------+-------------+--------+----------+----------+
| map_id | hit_name    | src1   | pos1     | pos2     |
+--------+-------------+--------+----------+----------+
|      1 | H0000000001 | hg19   | 22729300 |  2233890 |
|      2 | H0000000001 | hg19   | 22729400 |  2233990 |
|      3 | H0000000001 | hg19   | 22729500 |  2234090 |
|      4 | H0000000001 | gallus |  2233800 | 22729210 |
|      5 | H0000000001 | gallus |  2233900 | 22729310 |
+--------+-------------+--------+---------

Sincerely,
Hyunmin

켜짐 2014년 3월 31일 at 오후 8:58:43, Hyunmin Kim ([hidden email]) 작성됨:

http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=human;name=chr4:22729207..22729574

With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But,  remain unchanged

http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=human;name=chr4:22729207..22729574


켜짐 2014년 3월 25일 at 오후 4:53:17, Hyunmin Kim ([hidden email]) 작성됨:

Thanks for your reply.

I attached my error log file.

 One is that there are no alignments in the browser

Maybe, it bacause of test data. (my mistake)

The second is that no annotations (from the GFF) are visible for wild rice.

same reason. I didn’t prepare annotation data not yet.

anyway, I’ll try to re-set the gbrowse (synteny) with real my data. and I’ll report it for you.

Thanks.


켜짐 2014년 3월 19일 at 오후 5:39:18, Sheldon McKay ([hidden email]) 작성됨:

For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Sheldon McKay
Hi Hyunmin,

The error I am seeing looks like the search of the species' databases databases is not finding the reference sequences.  This can is sometimes caused by the reference sequence not being explicitly recorded in the GFF file.  Depending on the source of the GFF, each reference sequence should have a line in the GFF corresponding to the full sequence length.  In situations like yours, I usually add a header to the GFF that specified each reference sequence like so:

##gff-version 3
##sequence-region chr4 1 1497228

and then re-loading the Bio::DB::SeqFeature::Store database.  Note that there is one sequence-region line for each reference sequence in the GFF file and that the coordinates in the above example would need to be changed to those of your reference sequences.  

We can't see what is happening with the alignment data until the above problem is resolved.

Sheldon



On Mon, Mar 31, 2014 at 8:00 AM, Hyunmin Kim <[hidden email]> wrote:

With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But, remain the same (no result) Why? 

please confirm it.

mysql> select * from alignments LIMIT 5;
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
| hit_id | hit_name     | src1   | ref1 | start1    | end1      | strand1 | seq1 | bin          | src2   | ref2 | start2    | end2      | strand2 | seq2 |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
|      1 | H0000000001  | hg19   | chr4 |  22729207 |  22729574 | +       |      |  1000.022729 | gallus | 4    |   2233797 |   2234164 | +       |      |
|      2 | H0000000001r | gallus | 4    |   2233797 |   2234164 | +       |      | 10000.000223 | hg19   | chr4 |  22729207 |  22729574 | +       |      |
|      3 | H0000000002  | hg19   | chr4 | 110268510 | 110268621 | +       |      |  1000.110268 | gallus | 4    |   4431008 |   4431119 | +       |      |
|      4 | H0000000002r | gallus | 4    |   4431008 |   4431119 | +       |      |  1000.004431 | hg19   | chr4 | 110268510 | 110268621 | +       |      |
|      5 | H0000000003  | hg19   | chr4 | 170616761 | 170616846 | +       |      |  1000.170616 | gallus | 4    |   9653424 |   9653509 | +       |      |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
5 rows in set (0.00 sec)

mysql> select * from map LIMIT 5;
+--------+-------------+--------+----------+----------+
| map_id | hit_name    | src1   | pos1     | pos2     |
+--------+-------------+--------+----------+----------+
|      1 | H0000000001 | hg19   | 22729300 |  2233890 |
|      2 | H0000000001 | hg19   | 22729400 |  2233990 |
|      3 | H0000000001 | hg19   | 22729500 |  2234090 |
|      4 | H0000000001 | gallus |  2233800 | 22729210 |
|      5 | H0000000001 | gallus |  2233900 | 22729310 |
+--------+-------------+--------+---------

Sincerely,
Hyunmin

켜짐 2014년 3월 31일 at 오후 8:58:43, Hyunmin Kim ([hidden email]) 작성됨:


With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But,  remain unchanged



켜짐 2014년 3월 25일 at 오후 4:53:17, Hyunmin Kim ([hidden email]) 작성됨:

Thanks for your reply.

I attached my error log file.

 One is that there are no alignments in the browser

Maybe, it bacause of test data. (my mistake)

The second is that no annotations (from the GFF) are visible for wild rice.

same reason. I didn’t prepare annotation data not yet.

anyway, I’ll try to re-set the gbrowse (synteny) with real my data. and I’ll report it for you.

Thanks.


켜짐 2014년 3월 19일 at 오후 5:39:18, Sheldon McKay ([hidden email]) 작성됨:

For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Hyunmin Kim
As before, I can’t viewing the result in webpage.

My log …


[Mon Mar 31 21:52:08 2014] [error] [client 203.239.28.112] [Mon Mar 31 21:52:08 2014] Range.pm: Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251., referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/
[Mon Mar 31 21:52:39 2014] [error] [client 203.239.28.112] [Mon Mar 31 21:52:39 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/
[Mon Mar 31 21:52:40 2014] [error] [client 203.239.28.112] [Mon Mar 31 21:52:40 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/
[Mon Mar 31 21:52:40 2014] [error] [client 89.145.108.202] [Mon Mar 31 21:52:40 2014] Range.pm: Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
[Mon Mar 31 21:52:41 2014] [error] [client 203.239.28.112] File does not exist: /usr/share/gbrowse/htdocs/js/toggle.js, referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=human;name=chr4:22729207..22729574



I already added the gff file in config file.

Thanks,
Hyunmin

켜짐 2014년 3월 31일 at 오후 9:34:01, Sheldon McKay ([hidden email]) 작성됨:

Hi Hyunmin,

The error I am seeing looks like the search of the species' databases databases is not finding the reference sequences.  This can is sometimes caused by the reference sequence not being explicitly recorded in the GFF file.  Depending on the source of the GFF, each reference sequence should have a line in the GFF corresponding to the full sequence length.  In situations like yours, I usually add a header to the GFF that specified each reference sequence like so:

##gff-version 3
##sequence-region chr4 1 1497228

and then re-loading the Bio::DB::SeqFeature::Store database.  Note that there is one sequence-region line for each reference sequence in the GFF file and that the coordinates in the above example would need to be changed to those of your reference sequences.  

We can't see what is happening with the alignment data until the above problem is resolved.

Sheldon



On Mon, Mar 31, 2014 at 8:00 AM, Hyunmin Kim <[hidden email]> wrote:

With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But, remain the same (no result) Why? 

please confirm it.

mysql> select * from alignments LIMIT 5;
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
| hit_id | hit_name     | src1   | ref1 | start1    | end1      | strand1 | seq1 | bin          | src2   | ref2 | start2    | end2      | strand2 | seq2 |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
|      1 | H0000000001  | hg19   | chr4 |  22729207 |  22729574 | +       |      |  1000.022729 | gallus | 4    |   2233797 |   2234164 | +       |      |
|      2 | H0000000001r | gallus | 4    |   2233797 |   2234164 | +       |      | 10000.000223 | hg19   | chr4 |  22729207 |  22729574 | +       |      |
|      3 | H0000000002  | hg19   | chr4 | 110268510 | 110268621 | +       |      |  1000.110268 | gallus | 4    |   4431008 |   4431119 | +       |      |
|      4 | H0000000002r | gallus | 4    |   4431008 |   4431119 | +       |      |  1000.004431 | hg19   | chr4 | 110268510 | 110268621 | +       |      |
|      5 | H0000000003  | hg19   | chr4 | 170616761 | 170616846 | +       |      |  1000.170616 | gallus | 4    |   9653424 |   9653509 | +       |      |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
5 rows in set (0.00 sec)

mysql> select * from map LIMIT 5;
+--------+-------------+--------+----------+----------+
| map_id | hit_name    | src1   | pos1     | pos2     |
+--------+-------------+--------+----------+----------+
|      1 | H0000000001 | hg19   | 22729300 |  2233890 |
|      2 | H0000000001 | hg19   | 22729400 |  2233990 |
|      3 | H0000000001 | hg19   | 22729500 |  2234090 |
|      4 | H0000000001 | gallus |  2233800 | 22729210 |
|      5 | H0000000001 | gallus |  2233900 | 22729310 |
+--------+-------------+--------+---------

Sincerely,
Hyunmin

켜짐 2014년 3월 31일 at 오후 8:58:43, Hyunmin Kim ([hidden email]) 작성됨:


With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But,  remain unchanged



켜짐 2014년 3월 25일 at 오후 4:53:17, Hyunmin Kim ([hidden email]) 작성됨:

Thanks for your reply.

I attached my error log file.

 One is that there are no alignments in the browser

Maybe, it bacause of test data. (my mistake)

The second is that no annotations (from the GFF) are visible for wild rice.

same reason. I didn’t prepare annotation data not yet.

anyway, I’ll try to re-set the gbrowse (synteny) with real my data. and I’ll report it for you.

Thanks.


켜짐 2014년 3월 19일 at 오후 5:39:18, Sheldon McKay ([hidden email]) 작성됨:

For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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Re: Can't call method "get_feature_by_name" on an undefined value. (GBrowse_syn)

Sheldon McKay
It is not clear from your message whether you tried fixing the GFF.  Also, the error log makes me curious about your configuration files.  Could you share your current config files and a sample of the GFF?


On Mon, Mar 31, 2014 at 8:53 AM, Hyunmin Kim <[hidden email]> wrote:
As before, I can’t viewing the result in webpage.

My log …


[Mon Mar 31 21:52:08 2014] [error] [client 203.239.28.112] [Mon Mar 31 21:52:08 2014] Range.pm: Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251., referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/
[Mon Mar 31 21:52:39 2014] [error] [client 203.239.28.112] [Mon Mar 31 21:52:39 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/
[Mon Mar 31 21:52:40 2014] [error] [client 203.239.28.112] [Mon Mar 31 21:52:40 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/
[Mon Mar 31 21:52:40 2014] [error] [client 89.145.108.202] [Mon Mar 31 21:52:40 2014] Range.pm: Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
[Mon Mar 31 21:52:41 2014] [error] [client 203.239.28.112] File does not exist: /usr/share/gbrowse/htdocs/js/toggle.js, referer: http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=human;name=chr4:22729207..22729574



I already added the gff file in config file.

Thanks,
Hyunmin

켜짐 2014년 3월 31일 at 오후 9:34:01, Sheldon McKay ([hidden email]) 작성됨:

Hi Hyunmin,

The error I am seeing looks like the search of the species' databases databases is not finding the reference sequences.  This can is sometimes caused by the reference sequence not being explicitly recorded in the GFF file.  Depending on the source of the GFF, each reference sequence should have a line in the GFF corresponding to the full sequence length.  In situations like yours, I usually add a header to the GFF that specified each reference sequence like so:

##gff-version 3
##sequence-region chr4 1 1497228

and then re-loading the Bio::DB::SeqFeature::Store database.  Note that there is one sequence-region line for each reference sequence in the GFF file and that the coordinates in the above example would need to be changed to those of your reference sequences.  

We can't see what is happening with the alignment data until the above problem is resolved.

Sheldon



On Mon, Mar 31, 2014 at 8:00 AM, Hyunmin Kim <[hidden email]> wrote:

With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But, remain the same (no result) Why? 

please confirm it.

mysql> select * from alignments LIMIT 5;
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
| hit_id | hit_name     | src1   | ref1 | start1    | end1      | strand1 | seq1 | bin          | src2   | ref2 | start2    | end2      | strand2 | seq2 |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
|      1 | H0000000001  | hg19   | chr4 |  22729207 |  22729574 | +       |      |  1000.022729 | gallus | 4    |   2233797 |   2234164 | +       |      |
|      2 | H0000000001r | gallus | 4    |   2233797 |   2234164 | +       |      | 10000.000223 | hg19   | chr4 |  22729207 |  22729574 | +       |      |
|      3 | H0000000002  | hg19   | chr4 | 110268510 | 110268621 | +       |      |  1000.110268 | gallus | 4    |   4431008 |   4431119 | +       |      |
|      4 | H0000000002r | gallus | 4    |   4431008 |   4431119 | +       |      |  1000.004431 | hg19   | chr4 | 110268510 | 110268621 | +       |      |
|      5 | H0000000003  | hg19   | chr4 | 170616761 | 170616846 | +       |      |  1000.170616 | gallus | 4    |   9653424 |   9653509 | +       |      |
+--------+--------------+--------+------+-----------+-----------+---------+------+--------------+--------+------+-----------+-----------+---------+------+
5 rows in set (0.00 sec)

mysql> select * from map LIMIT 5;
+--------+-------------+--------+----------+----------+
| map_id | hit_name    | src1   | pos1     | pos2     |
+--------+-------------+--------+----------+----------+
|      1 | H0000000001 | hg19   | 22729300 |  2233890 |
|      2 | H0000000001 | hg19   | 22729400 |  2233990 |
|      3 | H0000000001 | hg19   | 22729500 |  2234090 |
|      4 | H0000000001 | gallus |  2233800 | 22729210 |
|      5 | H0000000001 | gallus |  2233900 | 22729310 |
+--------+-------------+--------+---------

Sincerely,
Hyunmin

켜짐 2014년 3월 31일 at 오후 8:58:43, Hyunmin Kim ([hidden email]) 작성됨:


With a example data in GBrowse (Gbrowse_syn), I changed it with my data. (Human chr4 vs gallus v4 in lastz)

But,  remain unchanged



켜짐 2014년 3월 25일 at 오후 4:53:17, Hyunmin Kim ([hidden email]) 작성됨:

Thanks for your reply.

I attached my error log file.

 One is that there are no alignments in the browser

Maybe, it bacause of test data. (my mistake)

The second is that no annotations (from the GFF) are visible for wild rice.

same reason. I didn’t prepare annotation data not yet.

anyway, I’ll try to re-set the gbrowse (synteny) with real my data. and I’ll report it for you.

Thanks.


켜짐 2014년 3월 19일 at 오후 5:39:18, Sheldon McKay ([hidden email]) 작성됨:

For the example data, there are two visible problems.  One is that there are no alignments in the browser. The second is that no annotations (from the GFF) are visible for wild rice.  I can not see any problems from the alignment database sample.  Did you load all of the GFF into the database for each species?  It would be helpful to see what is appearing in the apache error log when you try to load the page.

For the cat/tiger data.  The alignment database looks OK (apart from having only a single alignment in it).  Without seeing you configuration files, I am wondering if you are trying to load large GFF files into the in-memory adapter.  They would need to be in a mysql database if there are more than a few thousand lines.  Also, make sure they sequence names in the GFF match the sequence names in the alignment data exactly.  It would also helpful to see what appears in the apache error log.

Sheldon


On Tue, Mar 18, 2014 at 10:08 PM, Hyunmin Kim <[hidden email]> wrote:
I attached more database information.


mysql> use cat_synteny;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+-----------------------+
| Tables_in_cat_synteny |
+-----------------------+
| alignments            |
| map                   |
+-----------------------+
2 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   | chrI           | 176154 | 183558 | +       |      | 100000.000001 | tiger | tiger_Contig88 |  27212 |  30786 | +       |      |
|      2 | H000001r | tiger | tiger_Contig88 |  27212 |  30786 | +       |      | 100000.000000 | cat   | chrI           | 176154 | 183558 | +       |      |
+--------+----------+-------+----------------+--------+--------+---------+------+---------------+-------+----------------+--------+--------+---------+------+
2 rows in set (0.00 sec)

mysql> select * from map;
+--------+----------+-------+---------+---------+
| map_id | hit_name | src1  | pos1    | pos2    |
+--------+----------+-------+---------+---------+
|      1 | H000001  | cat   |  176154 |   27212 |
|      2 | H000001  | cat   |  177594 |   30786 |
|      3 | H000001  | cat   |  182118 |   27212 |
|      4 | H000001  | cat   |  183558 |   30786 |
|      5 | H000001  | tiger |   27212 |  176154 |
|      6 | H000001  | tiger |   30786 |  177594 |
|      7 | H000002  | cat   |  778780 |  539924 |
|      8 | H000002  | cat   |  786778 |  542961 |
|      9 | H000002  | cat   |  789497 |  533454 |
|     10 | H000002  | cat   |  799223 |  538726 |
|     11 | H000002  | tiger |  533454 |  789497 |
|     12 | H000002  | tiger |  538726 |  799223 |
|     13 | H000002  | tiger |  539924 |  778780 |
|     14 | H000002  | tiger |  542961 |  786778 |
|     15 | H000003  | cat   |  986150 |   37055 |
|     16 | H000003  | cat   |  989649 |   45600 |
|     17 | H000003  | cat   |  991428 |   29481 |
|     18 | H000003  | cat   |  994698 |   36608 |
|     19 | H000003  | tiger |   29481 |  991428 |
|     20 | H000003  | tiger |   36608 |  994698 |
|     21 | H000003  | tiger |   37055 |  986150 |
|     22 | H000003  | tiger |   45600 |  989649 |
|     23 | H000004  | cat   | 1453793 |  163110 |
|     24 | H000004  | cat   | 1456404 |  165414 |
|     25 | H000004  | cat   | 1456712 |  160849 |
|     26 | H000004  | cat   | 1457637 |  162712 |
|     27 | H000004  | cat   | 1458361 |  160204 |
|     28 | H000004  | cat   | 1459245 |  160815 |
|     29 | H000004  | cat   | 1459468 |  159346 |
|     30 | H000004  | cat   | 1459854 |  160000 |
|     31 | H000004  | cat   | 1459962 |  156183 |
|     32 | H000004  | cat   | 1461931 |  159022 |
|     33 | H000004  | tiger |  156183 | 1459962 |
|     34 | H000004  | tiger |  159022 | 1461931 |
|     35 | H000004  | tiger |  159346 | 1459468 |
|     36 | H000004  | tiger |  160000 | 1459854 |
|     37 | H000004  | tiger |  160204 | 1458361 |
|     38 | H000004  | tiger |  160815 | 1459245 |
|     39 | H000004  | tiger |  160849 | 1456712 |
|     40 | H000004  | tiger |  162712 | 1457637 |
|     41 | H000004  | tiger |  163110 | 1453793 |
|     42 | H000004  | tiger |  165414 | 1456404 |
|     43 | H000005  | cat   | 1727664 |  610136 |
|     44 | H000005  | cat   | 1729099 |  612845 |
|     45 | H000005  | cat   | 1729836 |  608798 |
|     46 | H000005  | cat   | 1731910 |  609918 |
|     47 | H000005  | tiger |  608798 | 1729836 |
|     48 | H000005  | tiger |  609918 | 1731910 |
|     49 | H000005  | tiger |  610136 | 1727664 |
|     50 | H000005  | tiger |  612845 | 1729099 |
+--------+----------+-------+---------+---------+
50 rows in set (0.00 sec)


Hyunmin

켜짐 2014년 3월 19일 at 오전 11:06:37, Hyunmin Kim ([hidden email]) 작성됨:



[root@han syn_demo]# pwd
/var/lib/gbrowse2/databases/syn_demo
[root@han syn_demo]# tree
.
├── alignments
│   └── gbrowse_synteny_coordinate.txt
├── cat
│   └── cat.gff3
└── tiger
    └── tiger.gff3

3 directories, 3 files

[root@han test]# pwd
/etc/gbrowse2/test
[root@han test]# tree
.
├── cat_synteny.conf
├── syn_demo.synconf
└── tiger_synteny.conf

0 directories, 3 files

[root@han gb2]# pwd
/var/www/cgi-bin/gb2
[root@han gb2]# tree
.
├── das
├── gbgff
├── gbrowse
├── gbrowse_details
├── gbrowse_gmap
├── gbrowse_img
├── gbrowse_key_img
├── gbrowse_login
├── gbrowse_syn
└── test_syn

0 directories, 10 files

I copied gbrowse_syn to test_syn and modified this content in below.

[root@han gb2]# diff gbrowse_syn test_syn
9c9
< our $CONF_DIR  = "$ENV{GBROWSE_CONF}/synteny";
---
> our $CONF_DIR  = "$ENV{GBROWSE_CONF}/test";


I success the viewing on web. but I can’t loading a track normally.

I attached *.conf (3 files)


But, I can’t load the my example data. Below is error message after has an long loading time..


Gateway Time-out

The gateway did not receive a timely response from the upstream server or application.


Apache/2.2.15 (CentOS) Server at www.hanjunghun.com Port 80


Thanks,
Hyumin

켜짐 2014년 3월 18일 at 오전 5:00:18, Sheldon McKay ([hidden email]) 작성됨:

I am terribly sorry about the slow response.  There is not enough information in your message to identify the problem.  One thing that comes to mind is that the gbrowse_syn_load_alignments_msa.pl script is for loading multiple sequence alignmants, not tab-delimited files.  However, you have at least two problems. ine with mapping data and one with one of your species databases.  Could you please provide sample data, if possible, and any other information you have?

Sheldon McKay


On Tue, Feb 18, 2014 at 8:26 AM, Hyunmin Kim <[hidden email]> wrote:
I have two question.

1. When I tried to use the gbrowse_syn, I got the below error.

Can't call method "get_feature_by_name" on an undefined value.

What happened? 

2. I have a custom tab-deliminated file (two species block information). and I’m imported the custom file set into mysql db using gbrowse_syn_load_alignments_msa.pl
Refere to attached file.

Up: example data in mysql database (GBrowse_syn package)
Down: my custom data in mysql database 

Is this result right? Why truncated in map table?

Sorry for my english.

Thanks,
Hyunmin

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