32- vs 64- Discrepancy

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Tim Olson

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Mar 2, 2015, 12:09:36 AM3/2/15
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We are running a --fast-epistasis analysis and noticed that the results differ whether we use the 32-bit version or 64-bit version of PLINK 1.9.  The 64-bit version seems to give reasonable results, but the 32-bit version, running on the same data, gives much lower p-values.  We have seen p-values from the 32-bit version as low as 1e-100 which is just crazy.  Note that we are also using the set x set feature, specifying a .set file with two sets of SNPs.  The exe versions in question are:

PLINK v1.90b3c 64-bit (2 Feb 2015)
PLINK v1.90b3c 32-bit (2 Feb 2015)

Unfortunately, we cannot share the data in question, but we have been able to repeat this problem with multiple datasets.

Tim Olson

Christopher Chang

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Mar 2, 2015, 12:57:17 AM3/2/15
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Okay, I'll try to reproduce this.  Can you post a sample log file from a bugged 32-bit run, so I know the dataset and set sizes in question, etc.?

Christopher Chang

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Mar 2, 2015, 5:04:57 AM3/2/15
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The March 2 development build includes a set-processing bugfix, which may or may not be related to the problem you're observing.

If it does not fix the problem, I'll need some more information to reproduce it.  I tried generating several synthetic datasets large enough to cause 32-bit integer overflows on various dimensions, and I wasn't able to get my 32-bit --fast-epistasis set-by-set results to diverge from my 64-bit results.


On Sunday, March 1, 2015 at 9:09:36 PM UTC-8, Tim Olson wrote:

Tim Olson

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Mar 2, 2015, 1:23:37 PM3/2/15
to Christopher Chang, plink...@googlegroups.com, Alexei Saltanov
The dev build 1.90p exhibits the same problem.  I should note that we are running the Windows build not Linux.  I have included the command-line we are using as well as the logs from 32- and 64- bit runs for both the stable and dev builds.  I'm also sharing our SET file since it's not sensitive.  If you still can't reproduce the issue, maybe we can synthesize a dataset which has the problem.

plink.exe --fast-epistasis --bfile 0004b6a4-4557-445f-b72f-2da6200c07a0 --fam 1d186cd0-9512-4a03-82de-d764c36e4d99.fam --set 0004b6a4-4557-445f-b72f-2da6200c07a0.set --out 0004b6a4-4557-445f-b72f-2da6200c07a0



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dev_32.log
dev_64.log
stable_32.log
stable_64.log
0004b6a4-4557-445f-b72f-2da6200c07a0.set

Christopher Chang

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Mar 4, 2015, 3:35:07 AM3/4/15
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Still haven't been able to reproduce the problem, so yes, a synthetic dataset which exhibits the discrepancy on your end would be helpful.
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Christopher Chang

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Mar 5, 2015, 8:40:28 PM3/5/15
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Bug should be fixed in the March 5 builds; thanks for the help.

Tim Olson

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Mar 5, 2015, 8:57:05 PM3/5/15
to Christopher Chang, Alexei Saltanov, plink...@googlegroups.com

Thank YOU for the help!

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