Hi Hiram,
Thanks for your advice.
Some new problems appear after "Click here to reset the browser user interface
settings to their defaults",
then go to mm8, mm9 or hg18, similar error come on for table 'mrna', error
message below:
--------------------mm8
Can't start query:
select * from mrna where tName='chr12' and (bin=1024 or bin=127 or bin=15 or
bin=1 or bin=0 or bin=4681 ) and tStart<57630019 and tEnd>57612908
mySQL error 1146: Table 'mm8.mrna' doesn't exist
---------------------mm9
Can't start query:
select * from mrna where tName='chr12' and (bin>=1025 and bin<=1026 or bin=128
or bin=15 or bin=1 or bin=0 or bin=4681 ) and tStart<57815592 and tEnd>57795962
mySQL error 1146: Table 'mm9.mrna' doesn't exist
--------------------hg18
Can't start query:
select * from mrna where tName='chrX'
and (bin>=1737 and bin<=1739 or bin=217 or bin=27 or bin=3 or bin=0
or bin=4681 )
and tStart<151383976 and tEnd>151073053
mySQL error 1146: Table 'hg18.mrna' doesn't exist
I already checked database, corresponding table like '_mrna' existed, please
see attachment.
Please give me some advice
Thanks & Regards
Wuqi
-----Original Message-----
From: Hiram Clawson [mailto:[email protected]]
Sent: Wednesday, March 16, 2011 10:23 PM
To: WANG Wuqi
Cc: [email protected]
Subject: Re: [Genome] Upgrade UCSC genome browser
Please do not run the make of trackDb in the source tree.
Move your private track .ra files out of the source tree
and follow the instructions in src/product/README.trackDb
Plus, it appears your binary hgTrackDb is out of date.
If you have a new source tree, build all of the utilities
and track loaders.
--Hiram
----- Original Message -----
From: "WANG Wuqi" <[email protected]>
To: "Hiram Clawson" <[email protected]>
Cc: [email protected], "WANG Wuqi" <[email protected]>
Sent: Tuesday, March 15, 2011 11:03:01 PM
Subject: RE: [Genome] Upgrade UCSC genome browser
Hi Hiram,
Thanks a lot. Previous problems already are fixed depending on your advice.
I already upgraded Genome browser from v218 to v247 with MySQL 5.1.54.
In my source tree, I still use old directory .../trackDb/*,
this is because I have myself customer data, and I can upload data
but to encounter when I compile, error message the following:
...............................................................
$ cd /home/wangp/jksrc/kent/src/hg/makeDb/trackDb
$ make alpha DBS=hg18
find . -type l -exec rm {} \;
./loadTracks -release=alpha trackDb hgFindSpec hg18
hgTrackDb -priority=human/priority.ra -release=alpha human hg18 trackDb
../../lib/trackDb.sql .
-priority is not a valid option
make: *** [alpha] Error 255
...............................................................
Please give me some advice
Best & Regards
Wuqi
-----Original Message-----
From: Hiram Clawson [mailto:[email protected]]
Sent: Wednesday, March 16, 2011 7:27 AM
To: WANG Wuqi
Cc: [email protected]
Subject: Re: [Genome] Upgrade UCSC genome browser
Good Afternoon:
Please edit the src/hg/hgTables/makefile and remove
the --executability argument from the rsyncDataOpts list.
If you encounter this again in a different makefile, perform
the same edit. We will be removing this argument from
the source tree.
--Hiram
=================================================================
To encounter the following errors when I upgrade this genome browser from
version 218 to 247:
$ cd jksrc/kent/src/hg
$ make compile
$ make install
...,
chmod g+w hgTables
chmod a+rx hgTables
rm -f /var/www/var/www/hgTables
mv hgTables /var/www/var/www/hgTables
rm -f /var/www/var/www/all.joiner
cp ../makeDb/schema/all.joiner /var/www/var/www
rm -rf /var/www/var/www/greatData
rsync --times --recursive --executability --omit-dir-times --cvs-exclude
--delete greatData /var/www/var/www/
rsync: --executability: unknown option
rsync error: syntax or usage error (code 1) at main.c(1084)
make[1]: *** [install] Error 1
make[1]: Leaving directory `/home/wangp/jksrc/kent/src/hg/hgTables'
make: *** [hgTables.install] Error 2
$ hgsql -e "show databases;" hg18
$ hgsql -e "show tables;" hg18 | grep -i mrna
$ mysql -uroot -p -A -e "show tables;" hg18 | grep _mrna | wc -l
HInvGeneMrna
all_mrna
chr10_mrna
chr10_random_mrna
chr11_mrna
chr11_random_mrna
chr12_mrna
chr13_mrna
chr13_random_mrna
chr14_mrna
chr15_mrna
chr15_random_mrna
chr16_mrna
chr16_random_mrna
chr17_mrna
chr17_random_mrna
chr18_mrna
chr18_random_mrna
chr19_mrna
chr19_random_mrna
chr1_mrna
chr1_random_mrna
chr20_mrna
chr21_mrna
chr21_random_mrna
chr22_h2_hap1_mrna
chr22_mrna
chr22_random_mrna
chr2_mrna
chr2_random_mrna
chr3_mrna
chr3_random_mrna
chr4_mrna
chr4_random_mrna
chr5_h2_hap1_mrna
chr5_mrna
chr5_random_mrna
chr6_cox_hap1_mrna
chr6_mrna
chr6_qbl_hap2_mrna
chr6_random_mrna
chr7_mrna
chr7_random_mrna
chr8_mrna
chr8_random_mrna
chr9_mrna
chr9_random_mrna
chrM_mrna
chrX_mrna
chrX_random_mrna
chrY_mrna
encodeEgaspFullPairagonMrna
knownGeneMrna
mgcFullMrna
mrnaClone
mrnaOrientInfo
mrnaRefseq
orfeomeMrna
spMrna
transMapAlnMRna
transMapInfoMRna
xenoMrna
[email protected]$ mysql -uroot -p -A -e "show tables;" hg18 | grep _mrna
| wc -l
Enter password:
50
mysql -uroot -p -A -e "show tables;" hg18 | grep _mrna | wc -l
[email protected]$ mysql -uroot -p -A -e "show tables;" hg18 | grep -v
"encode|wgEncode|CU" | wc -l
8110
----------------------mm8
[email protected]$ hgsql -e "show tables;" mm8 | grep -i mrna
all_mrna
all_mrna_new
chr10_mrna
chr10_random_mrna
chr11_mrna
chr12_mrna
chr13_mrna
chr13_random_mrna
chr14_mrna
chr15_mrna
chr15_random_mrna
chr16_mrna
chr17_mrna
chr17_random_mrna
chr18_mrna
chr19_mrna
chr1_mrna
chr1_random_mrna
chr2_mrna
chr3_mrna
chr4_mrna
chr5_mrna
chr5_random_mrna
chr6_mrna
chr7_mrna
chr7_random_mrna
chr8_mrna
chr8_random_mrna
chr9_mrna
chr9_random_mrna
chrM_mrna
chrUn_random_mrna
chrX_mrna
chrX_random_mrna
chrY_mrna
chrY_random_mrna
dupSpMrna
knownGeneMrna
mgcFullMrna
mrnaClone
mrnaOrientInfo
mrnaRefseq
spMrna
xenoMrna
[email protected]$ hgsql -e "show tables;" mm8 | grep -i mrna|wc -l
44
---------------------mm9
[email protected]$ hgsql -e "show tables;" mm9 | grep -i mrna
all_mrna
chr10_mrna
chr11_mrna
chr12_mrna
chr13_mrna
chr13_random_mrna
chr14_mrna
chr15_mrna
chr16_mrna
chr16_random_mrna
chr17_mrna
chr17_random_mrna
chr18_mrna
chr19_mrna
chr1_mrna
chr1_random_mrna
chr2_mrna
chr3_mrna
chr3_random_mrna
chr4_mrna
chr4_random_mrna
chr5_mrna
chr5_random_mrna
chr6_mrna
chr7_mrna
chr7_random_mrna
chr8_mrna
chr8_random_mrna
chr9_mrna
chr9_random_mrna
chrM_mrna
chrUn_random_mrna
chrX_mrna
chrX_random_mrna
chrY_mrna
chrY_random_mrna
knownGeneMrna
mgcFullMrna
mrnaClone
mrnaOrientInfo
transMapAlnMRna
transMapInfoMRna
xenoMrna
[email protected]$ hgsql -e "show tables;" mm9 | grep -i mrna|wc -l
43
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