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
