Hi Kyle, Thanks for sending the output of those commands -- that confirms that you have the same /gbdb/hg18/snp/snp130.fa and same hg19.snp130Seq as we do (that mysql output was from hg19, right?). Next, can you please send the output of this mysql command?
select settings from trackDb where tableName = "snp130"; Also, can you reproduce the error for rs72477211 (first SNP on chr1) and rs242 (first SNP in snp130.fa) and send the exact error messages? Angie > 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 > ------------------------------ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
