Hi Kyle,
I think I know what it is now: snp130.fa is an extremely large file, and either
your operating system can't handle its size or perhaps the flags
"-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE" were omitted from the build? (our
makefiles all include kent/src/inc/common.mk, which defines the variable
HG_DEFS to include those, and our compile rule uses $HG_DEFS)
snp130.fa is a whopping 18,668,682,162 bytes. (18GB or 17GiB depending on how
you count) If your filesystem can handle only 32-bit file offsets (or even 36),
that is just too big.
rs72477211 's offset ("select file_offset from snp130Seq where acc =
'rs72477211'") is 17524345321, which is (16 * 1024 * 1024 * 1024) + 344476137,
and 344476137 is the file offset that you see in the error message because the
top bit of the offset is lost.
What operating system and compiler are you using?
Angie
----- "Kyle Tretina" <[email protected]> wrote:
> From: "Kyle Tretina" <[email protected]>
> To: "Angie Hinrichs" <[email protected]>, "UCSC" <[email protected]>,
> "John Hayward" <[email protected]>
> Sent: Sunday, June 6, 2010 10:59:57 AM GMT -08:00 US/Canada Pacific
> Subject: Re: [Genome] Fwd: Fwd: Problem with Mirror
>
> Hello,
>
>
Note: this was in database hg19 using the command: select settings from trackDb
where tableName = "snp130";
=======================================================================
>
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| settings |
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| chimpDb panTro2
chimpOrangMacOrthoTable snp130OrthoPt2Pa2Rm2
codingAnnoLabel_snp130CodingDbSnp dbSNP
codingAnnotations snp130CodingDbSnp,
defaultGeneTracks knownGene
group varRep
hapmapPhase III
longLabel Simple Nucleotide Polymorphisms (dbSNP build 130)
macaqueDb rheMac2
maxWindowToDraw 10000000
orangDb ponAbe2
priority 100.094
shortLabel SNPs (130)
snpSeqFile /gbdb/hg18/snp/snp130.fa
track snp130
type bed 6 +
url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
urlLabel dbSNP:
visibility dense
|
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
1 row in set (0.07 sec)
>
>
=======================================================================
(This is the error message for rs72477211)
>
Error(s):
• Expected FASTA header, got this line: > ATAATACATT TTAATTTTCT AGAAAGTAAT
GGTATGAAGT TCCAACTTTT TTTAAAAAAG ACTTTTTTTC > at offset 344476137 in file
/gbdb/hg18/snp/snp130.fa
=======================================================================
>
So rs242 does work. When I enter it into my mirror, I am getting the same
output as your website. I was shocked when I saw it, because this was the first
one I had entered that did not return an error message.
>
>
Kyle Tretina
Wheaton College
>
>
>
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