Backing off a little bit. Ignore your special track for the moment. Does anything at all show up in your browser screen ? Is the genome browser drawing the display ? Can you navigate to the "base" view and see the DNA sequence of the genome in the browser in the base track ? Does the gap track function properly ?
Do you see a visibility control button for your track in the genome browser visibility controls ? Which group of buttons is it in ? --Hiram Tiandao Li wrote: > Answers from local DBA: > > These accesses to trackDb_wigExample are listed in the error_log after I > visit that page > > > [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] SELECT 1 FROM > trackDb_wigExample LIMIT 0 > [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] SELECT 1 FROM > trackDb_wigExample LIMIT 0 > [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] select * from > trackDb_wigExample where tableName = 'chromInfo' > [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] SELECT 1 FROM > trackDb_wigExample LIMIT 0 > [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] select * from > trackDb_wigExample > > Without the JKSQL_TRACE=on, I see no entries in the error log. > > > > On Thu, May 6, 2010 at 12:29 PM, Tiandao Li <[email protected]> wrote: > >> I contacted local DBA to solve this Apache errors. >> >> >> On Thu, May 6, 2010 at 12:26 PM, Hiram Clawson <[email protected]> wrote: >> >>> You may find them in: >>> /var/log/httpd/ >>> or maybe: /var/www/logs/ >>> or maybe: /etc/httpd/logs/ >>> >>> Something like that. Look for apache conf files in: >>> /etc/httpd/conf/httpd.conf >>> the concatenation of ServerRoot and ErrorLog will be the location of >>> the error log file: >>> >>> $ egrep "^ServerRoot|^ErrorLog" /etc/httpd/conf/httpd.conf >>> >>> --Hiram >>> >>> >>> Tiandao Li wrote: >>> >>>> mysql> select tableName from trackDb_wigExample; >>>> ......... >>>> .......... >>>> | zhaoLabRestingNucleosomeRevWig | >>>> | zhaoLabRestingUnphosPolII | >>>> | zhaoLabRestingUnphosPolIIBedGraph | >>>> +------------------------------------------------------------------+ >>>> 4374 rows in set (0.01 sec) >>>> >>>> I opened our website >>>> >>>> http://research.icts.uiowa.edu/genomebrowser/cgi-bin/hgTracks?db=hg18&JKSQL_TRACE=on >>>> >>>> looks like nothing changed. >>>> >>>> Where should I look for Apache error logs on EL5? >>>> >>>> Thanks, >>>> >>>> Tiandao >>>> >>>> On Thu, May 6, 2010 at 12:11 PM, Hiram Clawson <[email protected]> >>>> wrote: >>>> >>>> Good Morning Tiandao: >>>>> What do you see if you dump the contents of your trackDb_wigExample >>>>> table: >>>>> >>>>> mysql> select tableName from trackDb_wigExample; >>>>> >>>>> While viewing your genome browser where you expect the track to appear, >>>>> take a look at your Apache error logs to see if there are any unusual >>>>> errors being printed out. >>>>> >>>>> When viewing your genome browser, add this variable JKSQL_TRACE=on to >>>>> the >>>>> URL in >>>>> your WEB browser address: >>>>> http://your.domain.com/cgi-bin/hgTracks?db=hg18&JKSQL_TRACE=on >>>>> >>>>> Take a look at your Apache error log and see if there are any SQL >>>>> operations >>>>> begin performed with your trackDb_wigExample table. >>>>> >>>>> --Hiram >>>>> >>>>> Tiandao Li wrote: >>>>> >>>>> Hi, >>>>>> We installed a local genome browser with minimal installation. I tried >>>>>> to >>>>>> load wig files to local database. >>>>>> >>>>>> First, use wigEncode to make wig/wib files. >>>>>> >>>>>> l...@test01:~$ wigEncode PolII_eland_sorted2.wig PolII.wig PolII.wib >>>>>> Converted PolII_eland_sorted2.wig, upper limit 4385.00, lower limit >>>>>> 2.00 >>>>>> >>>>>> 2. mkdir wib folder inside of /mnt/nfs/genomdata/gbdb/hg18/ >>>>>> >>>>>> 3. [l...@research ~]$ /opt/kent/hgLoadWiggle >>>>>> -pathPrefix=/mnt/nfs/genomdata/gbdb/hg18/wib hg18 wigExample PolII.wig >>>>>> Connected to database hg18 for track wigExample >>>>>> Creating wiggle table definition in hg18.wigExample >>>>>> Saving wiggle.tab >>>>>> WARNING: Exceeded chrM size 16624 > 16571. dropping 3 data point(s) >>>>>> Loading hg18 >>>>>> >>>>>> 4. [l...@research ~]$ cp PolII.wib /mnt/nfs/genomdata/gbdb/hg18/wib/ >>>>>> >>>>>> 5. [l...@research trackDb]$ cd bin/kent/src/hg/makeDb/trackDb >>>>>> [l...@research trackDb]$ /opt/kent/hgTrackDb human hg18 >>>>>> trackDb_wigExample >>>>>> ../../lib/trackDb.sql . >>>>>> .... >>>>>> .... >>>>>> Loaded 4374 track descriptions total >>>>>> Loaded database hg18 >>>>>> >>>>>> 6. [l...@research trackDb]$ /opt/kent/hgFindSpec human hg18 >>>>>> hgFindspec_wigExample ../../lib/hgFindSpec.sql . >>>>>> found include file: ./human/hg18/trackDb.chainNet.ra >>>>>> found include file: ./human/hg18/trackDb.encode.ra >>>>>> found include file: ./human/hg18/trackDb.encodeGenes.ra >>>>>> found include file: ./human/hg18/trackDb.encodeTxLevels.ra >>>>>> found include file: ./human/hg18/trackDb.encodeChip.ra >>>>>> found include file: ./human/hg18/trackDb.encodeChrom.ra >>>>>> found include file: ./human/hg18/trackDb.encodeCompAndVar.ra >>>>>> found include file: ./human/hg18/trackDb.wgEncode.ra >>>>>> found include file: ./human/hg18/wgEncodeRikenCage.alpha.ra >>>>>> found include file: ./human/hg18/wgEncodeRikenCage.beta.ra >>>>>> found include file: ./human/hg18/wgEncodeCaltechRnaSeq.alpha.ra >>>>>> found include file: ./human/hg18/wgEncodeCaltechRnaSeq.beta.ra >>>>>> found include file: ./human/hg18/wgEncodeGisPet.alpha.ra >>>>>> found include file: ./human/trackDb.encode.ra >>>>>> found include file: ./human/trackDb.chainNet.ra >>>>>> found include file: ./trackDb.chainNet.ra >>>>>> Loaded 216 search specs total >>>>>> Loaded database hg18 >>>>>> >>>>>> 7. [l...@research trackDb]$ locate hg.conf >>>>>> /var/www/html/genomebrowser/cgi-bin/hg.conf >>>>>> >>>>>> vim /var/www/html/genomebrowser/cgi-bin/hg.conf >>>>>> >>>>>> change db.trackDb to >>>>>> >>>>>> db.trackDb=trackDb_wigExample,trackDb >>>>>> >>>>>> Now, I open local genome browser, still can't see my wigExample file. >>>>>> >>>>>> mysql> show tables; >>>>>> | wigExample | >>>>>> | xenoEst | >>>>>> | xenoMrna | >>>>>> | xenoRefFlat | >>>>>> | xenoRefGene | >>>>>> | xenoRefSeqAli | >>>>>> | yaleBertoneTars | >>>>>> +------------------------------------------------------------------+ >>>>>> >>>>>> mysql> select tableName from trackDb; >>>>>> >>>>>> | wgEncodeYaleChIPseqViewPeaks | >>>>>> | wgEncodeYaleChIPseqViewSignal | >>>>>> | wgRna | >>>>>> | xenoEst | >>>>>> | xenoMrna | >>>>>> | xenoRefGene | >>>>>> | yaleBertoneTars | >>>>>> +------------------------------------------------------------------+ >>>>>> >>>>>> Any help appreciate!!! >>>>>> >>>>>> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
