Hello, For the snp130.fa file I used, I believe that you said that we could only download that file from hg18, and that they used the same file in hg19, but did not move it into that directory. Everything else that I have I used hg19 except for the snp130.fa file.
Here is the requested info. ======= r...@ubuntu:/gbdb/hg19# ls -l total 1618876 -rw-r--r-- 1 root root 23601779 May 12 18:19 chr16.2bit -rw-r--r-- 1 root root 816241703 Jun 3 09:06 hg19.2bit -rw-rw-r-- 1 root root 816241703 Mar 8 2009 hg19.2bit.old drwxr-xr-x 2 root root 4096 Apr 22 17:33 html r...@ubuntu:/gbdb/hg19# diff hg19.2bit* r...@ubuntu:/gbdb/hg19# ls -lL /gbdb/hg18/snp/snp130.fa -rw-rw-r-- 1 root root 18668682162 May 15 2009 /gbdb/hg18/snp/snp130.fa r...@ubuntu:/gbdb/hg19# md5sum /gbdb/hg18/snp/snp130.fa feae327c42eabe801c1417928b3302fe /gbdb/hg18/snp/snp130.fa ======== mysql> show table status like "snp130Seq"; +-----------+--------+---------+------------+----------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+-------------------+----------+----------------+---------+ | Name | Engine | Version | Row_format | Rows | Avg_row_length | Data_length | Max_data_length | Index_length | Data_free | Auto_increment | Create_time | Update_time | Check_time | Collation | Checksum | Create_options | Comment | +-----------+--------+---------+------------+----------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+-------------------+----------+----------------+---------+ | snp130Seq | MyISAM | 10 | Dynamic | 17804034 | 23 | 427150548 | 281474976710655 | 269985792 | 0 | NULL | 2010-05-28 15:47:28 | 2010-05-28 15:56:30 | NULL | latin1_swedish_ci | NULL | | | +-----------+--------+---------+------------+----------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+-------------------+----------+----------------+---------+ 1 row in set (0.45 sec) ======== Note: the first part also shows the size of the hg19.2bit file downloaded May 8 is the same as the one we re-downloaded yesterday. Kyle Tretina Wheaton College ------------------------------ On Wed, Jun 2, 2010 at 3:19 PM, Jennifer Jackson <[email protected]> wrote: > Hello again Kyle, > > There could be one more problem. Did you mean hg18 or hg19? If you are > using the hg18 database, then the file hg18.2bit is the one you should be > using. > > If you could send some more info, that would be helpful, too. > > Please send us the output of these commands: > > % ls -lL /gbdb/hg18/snp/snp130.fa > > % md5sum /gbdb/hg18/snp/snp130.fa > > [If you don't have md5sum, don't worry about that one] > > Also, please send us the output of this SQL command: > > show table status like "snp130Seq"; > > If you have compiled the whole kent/src tree, and have ~/bin/$MACHTYPE in > your path, and have a ~/.hg.conf file set up (ask if you need help with > that) then you can use hgsql to execute the sql command like this: > > hgsql hg18 -e 'show table status like "snp130Seq";' > > Thanks Kyle, this should help us get a baseline so that we can resolve the > issues. > > > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 6/2/10 11:50 AM, Jennifer Jackson wrote: > >> Hi Kyle, >> >> Yes, this is likely the problem. hg19.2bit is required anyway for a >> minimal browser installation for the hg19 assembly. You can rsync the >> file from here: >> >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ >> >> Please try using the complete file and let us know if this solves the >> issue, >> >> Thanks, >> Jennifer >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> On 6/2/10 10:51 AM, Kyle Tretina wrote: >> >>> Hi Jennifer, >>> >>> When I loaded the data, I did not alter it; it is intact. As far as the >>> /gbdb files, snp130.fa was downloaded via rsync from /hg18 and >>> chr16.2bit was downloaded via ftp as chr16.fa and converted to a .2bit >>> file using the Blat-package program faToTwoBit. I then created a link to >>> chr16.2bit called "hg19.2bit". Perhaps this is where my problem is? As >>> far as the tables, I loaded all of the minimal tables as well as all of >>> the tables associated with the snp130 track, with no restrictions. >>> >>> Thanks, >>> >>> Kyle Tretina >>> Wheaton College >>> >>> >>> >>> On Tue, Jun 1, 2010 at 11:50 AM, Jennifer Jackson<[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> Hi Kyle, >>> >>> Very sorry to hear this procedure is still causing you problems. >>> Let's try to get it working. >>> >>> When you loaded the data (tables and /gbdb files), did you alter it >>> to restrict it to your chromosome of interest (chr16)? Or did you >>> leave everything intact (safest method)? >>> >>> It would probably be OK to limit to chr16 in the mySQL loaded >>> table(s) if you really need/want to, but do not alter the snp130.fa >>> file in /gbdb. If you do alter the /gbdb file, then the pointers in >>> the snp tables will not function correctly to retrieve data, which >>> sounds the problem. >>> >>> And to double check: all of the files are from the same >>> download/release cycle? >>> >>> Please let us know about the snp files/tables and we can follow up >>> from there, >>> >>> >>> Thank you, >>> Jennifer >>> >>> --------------------------------- >>> Jennifer Jackson >>> UCSC Genome Informatics Group >>> http://genome.ucsc.edu/ >>> >>> On 6/1/10 7:53 AM, Kyle Tretina wrote: >>> >>> To whom it may concern, >>> >>> So I have run the minimal browser installation using the scripts >>> that you >>> mentioned, and re-loaded the associated tables and I am still >>> receiving the >>> same error when I run a search for an rsnumber on my mirror. This >>> is >>> something to the effect of "Error: expected fasta header, got >>> this line - >>> (some combination of bases) at offset (some number) in file >>> /gbdb/hg18/snp/snp130.fa". I have been stuck with this issue for >>> a little >>> while now I would appreciate any help to be able to view the >>> alignments. >>> >>> >>> Thanks, >>> >>> >>> Kyle Tretina >>> Wheaton College >>> >>> >>> >>> >>> >>> >>> On Fri, May 14, 2010 at 4:23 PM, Hiram >>> Clawson<[email protected]<mailto:[email protected]>> wrote: >>> >>> Good Afternoon Kyle: >>> >>> What you probably want to do is run a minimal browser >>> installation >>> for the genome you want to work with. A minimal browser only >>> needs about six database tables to get started with and a >>> couple >>> of files in /gbdb/ >>> >>> Note the scripts in the source tree: >>> src/product/scripts/fetchMinimalGbdb.sh >>> src/product/scripts/fetchMinimalGoldenPath.sh >>> which can fetch just the files needed for a minimal browser. >>> >>> See also: >>> >>> http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation >>> >>> --Hiram >>> >>> >>> Kyle Tretina wrote: >>> >>> To whom it may concern, >>> >>> There was one area that was a little unclear in the >>> documentation when >>> creating a mirror for your site. I am only trying to >>> re-produce the >>> alignments for the track SNP(130). The data for gbdb, >>> which I have >>> re-downloaded twice and checked the file size for are: >>> >>> >>> /gbdb/hg18/snp/snp130.fa >>> >>> Also, under a link that Jennifer said would give us >>> direction for building >>> a >>> chr16 only database ( >>> >>> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database), >>> I >>> followed the instructions but was not sure what parts >>> should be included >>> because the page seems to be about a broader topic. >>> >>> What I did: >>> -Download chr16.fa from >>> >>> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ >>> -Convert chr16.fa to chr16.2bit using the BLAT-related >>> program faToTwoBit >>> (faToTwoBit chr16.fa chr16.2bit) >>> -Move chr16.2bit to the gbdb/hg19 area and create a link >>> to it called >>> "hg19.2bit" >>> >>> I did not continue on with these instructions because it >>> did not seem >>> appropriate to what I was doing (for example, I already >>> loaded the gold >>> and >>> gap tables from another step on the mirror procedures >>> page). Am I missing >>> something here? >>> >>> >>> Kyle Tretina >>> Wheaton College >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> <mailto:[email protected]> >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> >>> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
