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
