Updated Wiki: Home

November 14, 2014, 1:16 pm

≫ Next: Source code checked in, #111525

≪ Previous: New Post: Fatal Error : Expected phenotype indicator in file [allF2phe_plink.txt] near line 1:8 to be 0, 1, -9, or a floating point number.

$

0

0

We have moved to https://github.com/MicrosoftGenomics/FaST-LMM

---

Source code checked in, #111525

November 14, 2014, 9:54 pm

≫ Next: Updated Wiki: Documentation

≪ Previous: Updated Wiki: Home

$

0

0

Remove the files here to reduce confusion and re-direct people to FaST-LMM active development on http://github.com/MicrosoftGenomics/FaST-LMM

Updated Wiki: Documentation

November 14, 2014, 10:04 pm

≫ Next: Released: FaST-LMM development moved (Nov 12, 2014)

≪ Previous: Source code checked in, #111525

$

0

0

 

FaST-LMM development has moved to https://github.com/MicrosoftGenomics/FaST-LMM
and to minimize future confusion, we have removed the files from here.
Please join us on github.

 

Released: FaST-LMM development moved (Nov 12, 2014)

November 14, 2014, 10:07 pm

≫ Next: Updated Release: FaST-LMM development moved (Nov 12, 2014)

≪ Previous: Updated Wiki: Documentation

$

0

0

FaST-LMM development has moved to https://github.com/MicrosoftGenomics/FaST-LMM
and to minimize future confusion, we have removed the files from here.
Please join us on github.

Updated Release: FaST-LMM development moved (Nov 12, 2014)

November 14, 2014, 10:07 pm

≫ Next: Created Unassigned: Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356]. [21573]

≪ Previous: Released: FaST-LMM development moved (Nov 12, 2014)

$

0

0

FaST-LMM development has moved to https://github.com/MicrosoftGenomics/FaST-LMM
and to minimize future confusion, we have removed the files from here.
Please join us on github.

Created Unassigned: Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356]. [21573]

November 20, 2014, 2:02 am

≫ Next: Commented Unassigned: Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356]. [21573]

≪ Previous: Updated Release: FaST-LMM development moved (Nov 12, 2014)

$

0

0

Hi,
when I am trying to run FaSTLMM v2.07 on Unbuntu system with command:
fastlmmc -snpPairs -file cleanF2deChr0 -fileSim cleanF2deChr0 -extractSim foodfrequency.snps.txt -pheno test_phe.txt -pheno-name foodfrequency -out test.pairs.txt -tasks 250 0

I am getting the following output:
FastLmmC v2.07.20131102 - Factored Spectrally Transformed Linear Mixed Models [Release]
Copyright Microsoft Corporation -- Licensed Only for Non-Commercial use.
Compiled Nov 2 2013 at 20:09:57 by erg00lx for Linux v3.x kernel
using MKL v11.00.04 - Build: 20130517

++ Start Processing CommandLine:
-- Process -extract: [foodfrequency.snps.txt]
-- SnpIds found: 2048
-- End Processing CommandLine:

++ Start Loading FastLmm Data:
++ Start Loading Covariance Data:
++ Processing PLINK fileset: [cleanF2deChr0]
Warning : Found 'missing' phenotype marker. Excluding [4 8196] from the study
Warning : Found 'missing' phenotype marker. Excluding [4 8202] from the study
Warning : Found 'missing' phenotype marker. Excluding [4 8292] from the study
Warning : Found 'missing' phenotype marker. Excluding [4 9190] from the study
Warning : SNP[DRGA0000658] has no variation. Filtering SNP from dataset.
Warning : SNP[DRGA0000787] has no variation. Filtering SNP from dataset.
Warning : SNP[ALGA0003880] has no variation. Filtering SNP from dataset.
Number of Individuals Selected: 356
Number of Phenotypes: 1
Number of SNPs Read: 38067
Number of SNPs Used: 1810
-- End Processing PLINK fileset: [cleanF2deChr0]
-- End Loading Test Data:

-- End Loading FastLmm Data:

Compute/Load EigenSym:
Warning : The kernel has a few Eigenvalues that are a tiny bit smaller
than zero and are considered to be numerically zero.
Warning : Make the kernel positive semi definite.
Warning : Setting negative eigenvalues to zero.
Compute GWAS using LMM:
Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356].

Am I missing something or doing something wrong?
Best regards,
feng zhang

Commented Unassigned: Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356]. [21573]

November 21, 2014, 10:35 am

≪ Previous: Created Unassigned: Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356]. [21573]

$

0

0

Hi,
when I am trying to run FaSTLMM v2.07 on Unbuntu system with command:
fastlmmc -snpPairs -file cleanF2deChr0 -fileSim cleanF2deChr0 -extractSim foodfrequency.snps.txt -pheno test_phe.txt -pheno-name foodfrequency -out test.pairs.txt -tasks 250 0

I am getting the following output:
FastLmmC v2.07.20131102 - Factored Spectrally Transformed Linear Mixed Models [Release]
Copyright Microsoft Corporation -- Licensed Only for Non-Commercial use.
Compiled Nov 2 2013 at 20:09:57 by erg00lx for Linux v3.x kernel
using MKL v11.00.04 - Build: 20130517

++ Start Processing CommandLine:
-- Process -extract: [foodfrequency.snps.txt]
-- SnpIds found: 2048
-- End Processing CommandLine:

++ Start Loading FastLmm Data:
++ Start Loading Covariance Data:
++ Processing PLINK fileset: [cleanF2deChr0]
Warning : Found 'missing' phenotype marker. Excluding [4 8196] from the study
Warning : Found 'missing' phenotype marker. Excluding [4 8202] from the study
Warning : Found 'missing' phenotype marker. Excluding [4 8292] from the study
Warning : Found 'missing' phenotype marker. Excluding [4 9190] from the study
Warning : SNP[DRGA0000658] has no variation. Filtering SNP from dataset.
Warning : SNP[DRGA0000787] has no variation. Filtering SNP from dataset.
Warning : SNP[ALGA0003880] has no variation. Filtering SNP from dataset.
Number of Individuals Selected: 356
Number of Phenotypes: 1
Number of SNPs Read: 38067
Number of SNPs Used: 1810
-- End Processing PLINK fileset: [cleanF2deChr0]
-- End Loading Test Data:

-- End Loading FastLmm Data:

Compute/Load EigenSym:
Warning : The kernel has a few Eigenvalues that are a tiny bit smaller
than zero and are considered to be numerically zero.
Warning : Make the kernel positive semi definite.
Warning : Setting negative eigenvalues to zero.
Compute GWAS using LMM:
Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356].

Am I missing something or doing something wrong?
Best regards,
feng zhang
Comments: ** Comment from web user: heckerma **

Hi Feng Zhang,

This is a known limitation in the C++ version. It is fixed in the python version at https://github.com/MicrosoftGenomics/FaST-LMM.

Best,

David