Hello, For this particular rs72477211, we see the file offset in snp130Seq is 17524345321. On the web page, we see o=10259&t=10260. Is there a reasonable way, given the rsnumber, obtain the 'o' and 't' values?
Kyle Tretina On Tue, Jun 8, 2010 at 12:36 PM, Angie Hinrichs <[email protected]> wrote: > P.S. actually I would like to change "long offset = 0;" to "off_t offset = > 0;". getSnpSeqFileOffset already returns off_t so I believe that should > work fine on 32 bits with -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE . > > Thanks again, > > Angie > > > ----- "John Hayward" <[email protected]> wrote: > > From: "John Hayward" <[email protected]> > > To: "John Hayward" <[email protected]>, "Angie Hinrichs" < > [email protected]>, "Kyle Tretina" <[email protected]> > > Cc: "UCSC" <[email protected]> > > Sent: Tuesday, June 8, 2010 8:51:03 AM GMT -08:00 US/Canada Pacific > > > Subject: RE: [Genome] Fwd: Fwd: Problem with Mirror > > > > > > > > Hi Angie, > > We were able to get our queries to work after making changes to > getSnpSeqFileOffset > > function in hgc.c. It appears that the original code does not work in a > 32 bit environment. Here are the changes we needed to do to have it work in > our setting: > > 1) Line 23137 change declaration of offset > > === was > > long offset = 0; > > === to > > long long offset = 0; > > > > 2) Line 23135 change call of conversion of returned sql offset: > > ==== was > > offset = sqlUnsignedLong(row[0]) > > === to > > offset = sqlLongLong(row[0]) > > > > I don't know if there are other 32/64 issues but it may be helpful to > others working in a 32 bit environment to have these adjustments made in the > code. > > > > Thanks for your help in locating this problem. > > > > johnh... > > > > > ------------------------------ > > *From:* John Hayward > > *Sent:* Tuesday, June 08, 2010 9:51 AM > > *To:* Angie Hinrichs; Kyle Tretina > > *Cc:* UCSC > > *Subject:* RE: [Genome] Fwd: Fwd: Problem with Mirror > > > > > > > > The problem seems to be a 64/32 bit issue. > > I rebuilt the binaries and observed the flags for building (here is a > snippet) > > .... > > gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type > -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_i486 -Wall -Werror -Wformat -Wimplicit -Wreturn-type > -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc > -I../../../../../inc -o hgLoadWiggle.o -c hgLoadWiggle.c > > .... > > > > The error on the web page we see is: > > ===== > > Expected FASTA header, got this line: > > ATAATACATT TTAATTTTCT AGAAAGTAAT GGTATGAAGT TCCAACTTTT TTTAAAAAAG > ACTTTTTTTC > > at offset 344476137 in file /gbdb/hg18/snp/snp130.fa > > ====== > > The offset you are seeing from the database is 17524345321 > > > > Here is a bc script: > > ===== > > bc 1.06.94 > > Copyright 1991-1994, 1997, 1998, 2000, 2004, 2006 Free Software > Foundation, Inc. > > This is free software with ABSOLUTELY NO WARRANTY. > > For details type `warranty'. > > obase=16 > > 15 > > F > > 344476137 // this is the offset reported in the error > > 148849E9 > > 17524345321 // this is the offset according to the database > > 4148849E9 // if you truncate this value to 32 bits (last 8 hex digits) > then you get the value > > // above > > ====== > > This shows that the offset in the database is more than 32 bits and when > truncated to 32 bits is the same value reported in the error message. > > > > The operating system is: > > Linux ubuntu 2.6.31-302-ec2 #7-Ubuntu SMP Tue Oct 13 19:06:04 UTC 2009 > i686 GNU/Linux > > Ubuntu 10.04 (lucid) > > > > Now we need to find out where the offset is being truncated - it seems > that the flags for file offsets are in place but I wonder if there are some > other 32 bit issues in the source. > > > > I recall when originally building there were some warnings which required > some changes to compile. I think the next step is to repeat those steps and > make sure there are no 32/64 bit issues. > > > > johnh... > > > > > ------------------------------ > > *From:* Angie Hinrichs [[email protected]] > > *Sent:* Monday, June 07, 2010 5:26 PM > > *To:* Kyle Tretina > > *Cc:* UCSC; John Hayward > > *Subject:* Re: [Genome] Fwd: Fwd: Problem with Mirror > > > > > > 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 > > > > > > > > > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
