smartpca "bad anova popsizes too small"
petercombs opened this issue · comments
Okay, moving farther along in the pipeline, I'm having trouble getting smartpca to work properly (which I think is the first indication that I'm falling off the rails). Specifically, I get:
$ $hawkDir/smartpca -p $hawkDir/parfile.txt
... snip ....
## To get Tracy-Widom statistics: recompile smartpca with TWTAB correctly specified in Makefile, or
just run twstats (see README file in POPGEN directory)
kurtosis snps indivs
eigenvector 1 1.065 1.000
eigenvector 2 -nan -nan
population: 0 Case 2
population: 1 Control 0 ***
... more data ...
eigenvector 1:means
Case 0.000
Control 0.000
*** warning: bad anova popsizes too small
eigenvector 2:means
Case 0.000
Control 0.000
*** warning: bad anova popsizes too small
##end of smartpca run
Happy to figure out how to get copies of my gwas_eigenstratX*
files to you, but this is what they look like (in case the format of any of them seems way off):
$ head gwas_eigenstratX*
==> gwas_eigenstratX.geno <==
1 0
0 1
1 0
1 0
0 1
0 1
1 0
0 1
1 0
1 0
==> gwas_eigenstratX.ind <==
TSI_0 U Case
TSI_1 U Case
TSI_2 U Case
TSI_3 U Case
TSI_4 U Case
TSI_5 U Case
TSI_6 U Case
TSI_7 U Case
TSI_8 U Case
TSI_9 U Case
==> gwas_eigenstratX.snp <==
AAAAAAAAAAAAAAAAAAAAAAAGAGACCCC 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAACAATCAG 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAGATGTTGC 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAGGCGAACA 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAAACTTCTA 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAACCAAACGA 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAAGCTCTTA 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAACGAGGCT 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAAGGGATGG 1 0.000000 0
AAAAAAAAAAAAAAAAAAAAAAAAGCATACC 1 0.000000 0
==> gwas_eigenstratX.total <==
884693180
873243637
817020044
820305452
812869594
811915218
774600059
877385766
874686116
878343007
The format of the gwas_eigenstratX.geno file does seem off. There is supposed to be one column per each sample. Could you print caseCount and controlCount after line 14 in the following script (and comment out the rest) to check if HAWK is getting as input right numbers of cases and controls?
https://github.com/atifrahman/HAWK/blob/master/supplements/runHawk
Ah, it seems HAWK was not getting the right numbers as input... I had tweaked the script to set them both to 1 from a previous attempt at running HAWK on only 1 sample each, and didn't set it back.