Hi Kyle, You should be able to rsync the entire file located /gbdb/hb18/snp/snp130.fa and use it as-is. If you altered it after retrieval, this could be the root cause of the indexing problem.
Please try again with an intact file and let us know if the problem is not resolved, Thank you, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/10/10 1:06 PM, Kyle Tretina wrote: > To whom it may concern, > > I sent you an email some day last week, and have not been able to respond > because of class finals week. As I said before, I am attempting to create a > mirror of your website, using only chr16 and the snp130.fa to reproduce the > alignments. When I enter in an rsnumber, the graphic with the rsnumber in a > black box appears as expected. However, when I click on it to get to the > next page that should have the alignment, I instead get the following error > message: > > Expected FASTA header, got this line: > tgcgg tgacgggcgc > at offset 1632856238 in file /gbdb/hg18/snp/snp130.fa > > After re-downloading and re-loading the tables we are still getting the same > error. > > I would like to find out if the snp130.fa file that you use is somehow > different than what I have. If the file format is ascii and it is created > for a windows environment the line endings are different than unix (eg 2 > characters per line vs 1 character per line). I assume you are running on > unix boxes. Could check to find out if your snp130.fa file looks the same as > mine when I probe > for rs8063034? > > Can you do an octal dump on the file /gbdb/hb18/snp/snp130.fa to see if > you see the same or different than what we are seeing? - here is the od > script > ==== > jo...@ubuntu:/gbdb/hg18/snp$ od -c -A d --skip=1632856238 snp130.fa | more > 1632856238 t g c g g t g a c g g g c g c > 1632856254 \n c t g t a g t c c c a g c t > 1632856270 g c t c t g c a g g c t g a g > 1632856286 g c a g g a g a a t g g t g > 1632856302 t g a a c c c g g g a g g t g > .... > ==== > If you see something different then I need to focus on the download process > of the snp130.fa file - eg where I am getting it - how I download it. > If you see the same thing then I need to find out why I am looking in the > wrong place - if this is the case maybe you could include some debugging to > show where I should be looking in snp130.fa for this rs number? > > Kyle Tretina > Wheaton College > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
