Problems occur when adding custom track

98 views
Skip to first unread message

Min Ou

unread,
Oct 8, 2014, 12:12:32 PM10/8/14
to genome...@soe.ucsc.edu
​Dear Genome Browser Mirror Site Helper: 

I am trying to set up the mirror site of the UCSC genome browser and I need some help from you. Many thanks in advance :)

My server is CentOS release 6.3 64bit. Minimal Browser was installed. hgcentral (not empty), hg19 (not empty), customTrash (It is empty) database were set. 

On the page of localhost/cgi-bin/hgGateway, see the default.png, the default view can only display the base of the hg19 genome without other annotation tracks like dbSNP or transcript. Is this normal?

​

The SAMTABIX was downloaded and added to the ~/.bashrc. But I am not sure whether it works or not because I do not know how it was called by the browser and cannot find a way to test it.

Here are some problems I encountered when adding the custom track:
See Error1&2.png

​
Error 1:
Error Unrecognized format type=bam line 0 of NULL file

On localhost/cgi-bin/hgCustom page, I tried to add a custom track to display the BAM file but the error occurs. (using example one from http://genome.ucsc.edu/goldenpath/help/bam.html)

Also, another error is near the button of the page:
Error 2:
Program Error: Missing file /var/www/html/goldenPath/help/customTrackLoad.html
I am not sure whether error 2 will affect error 1.
On my server, there exists /var/www/html/goldenPath/help/ folder but does not exist the customTrackLoad.html file. Please tell me how to fix it. I guess the goldenPath folder comes from the htdocs folder download? Because I did not install it.

Problem 3: localhost/images/ folder is empty. I manually download some gif file from UCSC and put them inside. It worked. But I hope to find an efficient way to download all files in that folder.
I tried "rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ $WEBROOT/" at least 5 times but the image folder is still empty. $WEBROOT is set correctly.

Thank you so much for reading my email and help me solve the problems.

Best regards,
Min

Min Ou

unread,
Oct 9, 2014, 7:03:11 PM10/9/14
to genome...@soe.ucsc.edu
Dear Genome Browser Mirror Site Helper:

After the error 1 (in my previous email) occurred, if I click the submit button again, new errors occur:

​Below message is from the apache error log /var/log/httpd/error_log
[Thu Oct 09 11:15:05 2014] [error] [client 147.8.177.159] [Thu Oct  9 11:15:05 201] [hgCustom] [client 147.8.177.159] [hgsid=39_vrDd69U0cCQroqvZyIUu2] [/cgi-bin/hgCustom] Warning: central database genomeClade doesn't contain genome "Human", referer: http://bal21/cgi-bin/hgCustom
[Thu Oct 09 11:15:05 2014] [error] [client 147.8.177.159] [Thu Oct  9 11:15:05 201] [hgCustom] [client 147.8.177.159] [hgsid=39_vrDd69U0cCQroqvZyIUu2] [/cgi-bin/hgCustom] Can't start query:, referer: http://bal21/cgi-bin/hgCustom
[Thu Oct 09 11:15:05 2014] [error] [client 147.8.177.159] select name from dbDb where name = 'felCat3', referer: http://bal21/cgi-bin/hgCustom
[Thu Oct 09 11:15:05 2014] [error] [client 147.8.177.159] [Thu Oct  9 11:15:05 201] [hgCustom] [client 147.8.177.159] [hgsid=39_vrDd69U0cCQroqvZyIUu2] [/cgi-bin/hgCustom] mySQL error 2013: Lost connection to MySQL server during query (profile=<noProfile>, host=localhost, db=hgcentral)[Thu Oct  9 11:15:05 201] [hgCustom] [client 147.8.177.159] [hgsid=39_vrDd69U0cCQroqvZyIUu2] [/cgi-bin/hgCustom] nextRow failed[Thu Oct  9 11:15:05 201] [hgCustom] [client 147.8.177.159] [hgsid=39_vrDd69U0cCQroqvZyIUu2] [/cgi-bin/hgCustom] mySQL error 2013: Lost connection to MySQL server during query (profile=<noProfile>, host=localhost, db=hgcentral), referer: http://bal21/cgi-bin/hgCustom

I checked the database and the genomeClade contains genome Human.
Below are settings from hg.conf
User    Database-Access
db.user=ucsc_browser     SELECT, CREATE TEMPORARY TABLES ON hgcentral.*
customTracks.user=ucsc_custom     SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, ALTER ON customTrash.* & FILE ON *.*
central.user=ucsc_admin     SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, ALTER, CREATE TEMPORARY TABLES ON hgcentral.*
backupcentral.user=ucsc_admin
archivecentral.user=ucsc_admin

I followed the browser installation in below links:

And set up the custom track function by following step E in below link:

I searched in the UCSC Genome Browser mirror site discussion list and find one possible solution for the Error 1 in my previous email. It is said that SAMTABIX might be important so I installed it.
I installed the SAMTABIX following below link:
~/.bashrc is also modified:
export USE_SAMTABIX=1
export SAMDIR=/home/mou/samtabix
export SAMINC=${SAMDIR}
export SAMLIB=${SAMDIR}/libbam.a
export PATH=/var/www/html/kentUtils:.:$PATH

Here are the databases:
mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| customTrash        |
| hg19               |
| hgFixed            |
| hgcentral          |
| mysql              |
| test               |
+--------------------+

mysql> use hgcentral;
Database changed
mysql> show tables;
+---------------------+
| Tables_in_hgcentral |
+---------------------+
| blatServers         |
| clade               |
| dbDb                |
| dbDbArch            |
| defaultDb           |
| gbMembers           |
| genomeClade         |
| hubPublic           |
| hubStatus           |
| liftOverChain       |
| namedSessionDb      |
| sessionDb           |
| targetDb            |
| userDb              |
+---------------------+

mysql> select * from dbDb where name like "felCat3";
+---------+---------------------------+---------------+----------+---------------------------------+--------+----------+--------+----------------+-------------------------------------+----------+--------+-----------------+-------+
| name    | description               | nibPath       | organism | defaultPos                      | active | orderKey | genome | scientificName | htmlPath                            | hgNearOk | hgPbOk | sourceName      | taxId |
+---------+---------------------------+---------------+----------+---------------------------------+--------+----------+--------+----------------+-------------------------------------+----------+--------+-----------------+-------+
| felCat3 | Mar. 2006 (Broad/felCat3) | /gbdb/felCat3 | Cat      | scaffold_216010:162,840-178,893 |      1 |     2420 | Cat    | Felis catus    | /gbdb/felCat3/html/description.html |        0 |      0 | Broad Release 3 |  9685 |
+---------+---------------------------+---------------+----------+---------------------------------+--------+----------+--------+----------------+-------------------------------------+----------+--------+-----------------+-------+

mysql> select * from genomeClade where genome like 'human';
+--------+--------+----------+
| genome | clade  | priority |
+--------+--------+----------+
| Human  | mammal |        1 |
+--------+--------+----------+

Thank you very much.

Best regards,
Min

Luvina Guruvadoo

unread,
Oct 15, 2014, 3:59:29 PM10/15/14
to Min Ou, genome...@soe.ucsc.edu
Hello Min,

You can use the following join statements to verify the relationships between tables in your hgencentral database:
hgsql -N -e "SELECT distinct(c.name), c.label FROM
clade c, genomeClade g, dbDb d
WHERE c.name=g.clade AND d.organism=g.genome AND d.active=1
ORDER BY c.priority;" hgcentraltest

hgsql -N -e "SELECT name from clade order by priority;" hgcentraltest | \
while read C
do
    hgsql -N -e "SELECT c.name, g.genome, d.name FROM
clade c, genomeClade g, dbDb d
WHERE g.clade=\"$C\" AND c.name=g.clade AND
  d.organism=g.genome AND d.active=1;" hgcentraltest
done
The MySQL errors are probably due to your permission settings. Also, we do not recommend following the instructions you linked to on hybridstat.gr. Please refer to our help pages and wiki to make sure you have set up everything correctly:
http://genome.ucsc.edu/admin/mirror.html
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product

I should also mention that we are in the process of releasing a new product, the Genome Browser in a Box (GBiB), which you can read more about here: http://genome.ucsc.edu/goldenPath/help/gbib. We are currently in the final stages of testing the GBiB and plan to release it very soon. After it has been officially released, there will be a download link on the previously mentioned GBiB help page.

If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group


--


Reply all
Reply to author
Forward
0 new messages