is there a limit on qcovars for fastgwa ?

dvh13
New Member

Posts: 5

is there a limit on qcovars for fastgwa ? May 1, 2020 9:11:49 GMT

Quote

Post by dvh13 on May 1, 2020 9:11:49 GMT

I am trying to use age, age2, 20 PCs as qcovar in fastgwa-mlm

Keep getting errors when reading the qcovar file, see below:

It runs fine if I just specify age,age2

Is there a limit to the number of qcovars?
Or do I need to process them in some way (e.g. normalise) first?

thanks, david

*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.93.2b beta Linux
* (C) 2010-present, The University of Queensland
* Please report bugs to Jian Yang <jian.yang@uq.edu.au>
*******************************************************************

Reading quantitative covariates from [qcovar_age_age2_20PCs_gcta64_space.txt].
Warning: inconsistent column number in line 2 from [qcovar_age_age2_20PCs_gcta64_space.txt].
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted

dvh13
New Member

Posts: 5

is there a limit on qcovars for fastgwa ? May 1, 2020 11:55:15 GMT

Quote

Post by dvh13 on May 1, 2020 11:55:15 GMT

OK, beginners error:

gcta64 is very sensitive to file formatting. i thought i had converted from mac to linux, but must have missed something. i processed the qcovar file in awk and now it works fine with 20 PCs.

beware

these files ran fine in plink (copes with a lot of different formatting). but gcta64 does not !

dcornejo New Member Posts: 1	is there a limit on qcovars for fastgwa ? May 13, 2020 22:09:10 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by dcornejo on May 13, 2020 22:09:10 GMT Is there a way to know how the format of the files for this options are? --pheno phenotype.txt --qcovar pc.txt --covar fixed.txt Thank you

ax
New Member

Posts: 27

is there a limit on qcovars for fastgwa ? Jun 22, 2020 5:45:10 GMT

Quote

Post by ax on Jun 22, 2020 5:45:10 GMT

--pheno phenotype.txt

FID IID XXXXX
199200X 199200X 5.275
573118X 573118X 4.635
299027X 299027X 4.933
543615X 543615X 5.111

--qcovar pc.txt
FID IID age PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 PC17 PC18 PC19 PC20
100001X 100001X 76 -0.00116322 -0.000749452 0.000183477 -0.0007262 3.27253e-05 -0.00135422 0.00247636 0.000900967 0.000369554 -0.00319971 0.00192588 -0.000908054 0.000702194 0.00350161 0.00214818 -0.00228872 -0.00382498 0.00212115 -0.00651459 0.00206692

--covar fixed.txt
FID IID gender centre batch
100001X 100001X 1 11007 35
100002X 100002X 1 11009 49
100003X 100003X 0 11009 2
100004X 100004X 0 11009 5
100005X 100005X 0 11007 70

Post by dvh13 on May 1, 2020 9:11:49 GMT

Post by dvh13 on May 1, 2020 11:55:15 GMT

Post by dcornejo on May 13, 2020 22:09:10 GMT

Post by ax on Jun 22, 2020 5:45:10 GMT