Interpretation of results?

[PhilPalmer]

Hi,

I have cloned the repo & gone inside of the directory.

However, when I run make or make all I get the following error:

......
/usr/bin/ld: bcftools/libbcf.a(bcfutils.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:44: recipe for target 'samtools' failed
make[1]: *** [samtools] Error 1
make[1]: Leaving directory '/phil/iAdmix/parsebam/samtools-0.1.18'
Makefile:4: recipe for target 'all' failed
make: *** [all] Error 2

Any ideas what the problem may be?

Many thanks in advance, any help would be much appreciated

[PhilPalmer]

EDIT: I have got the build to run correctly now. I am not completely sure what the issue was before but its now resolved.

When I run the following command:

python ancestry/runancestry.py --plink 23andMe/uk35C650_20170608144013 -f data/refPanel_modernK16.txt -o test --path ancestry

I get the following stdout:

reading allele frequency file data/refPanel_modernK16.txt
reading mapfile 23andMe/uk35C650_20170608144013.map


ancestry admixture calculations for individual: 1 uk35C650_20170608144013 using 0 markers
difficult to estimate admixture coefficients with high confidence

final maxval 0.000000 ADMIX_PROP A1:0.084603 Westasian:0.037795 Austronesian:0.013093 Eastasian:0.048912 Siberian:0.020488 Onge:0.098053 Uralic:0.053994 Northeuropean:0.124891 Amerindian:0.054624 ASI:0.064810 AHG:0.058494 Southeastasian:0.097362 Eastafrican:0.067909 Neareast:0.071535 Sahul:0.005813 SSA:0.089954 Paleosiberian:0.007669
A1:0.0846:0.00 Westasian:0.0378:0.00 Austronesian:0.0131:0.00 Eastasian:0.0489:0.00 Siberian:0.0205:0.00 Onge:0.0981:0.00 Uralic:0.0540:0.00 Northeuropean:0.1249:0.00 Amerindian:0.0546:0.00 ASI:0.0648:0.00 AHG:0.0585:0.00 Southeastasian:0.0974:0.00 Eastafrican:0.0679:0.00 Neareast:0.0715:0.00 Sahul:0.0058:0.00 SSA:0.0900:0.00 Paleosiberian:0.0077:0.00 FINAL_ALL_PROPS
A1:0.0846:0.00 Westasian:0.0378:0.00 Austronesian:0.0131:0.00 Eastasian:0.0489:0.00 Siberian:0.0205:0.00 Onge:0.0981:0.00 Uralic:0.0540:0.00 Northeuropean:0.1249:0.00 Amerindian:0.0546:0.00 ASI:0.0648:0.00 AHG:0.0585:0.00 Southeastasian:0.0974:0.00 Eastafrican:0.0679:0.00 Neareast:0.0715:0.00 Sahul:0.0058:0.00 SSA:0.0900:0.00 Paleosiberian:0.0077:0.00 FINAL_NZ_PROPS bins 200 ssq 0.000000
LL 0.000000 LL_exp 0.000000 0.000000 -nan

And I get the following output:

test.uk35C650_20170608144013.input
test.uk35C650_20170608144013.input.ancestry

Has everything worked at expected?
Does the stdout show the estimated allele frequencies? If so how do I interpret them and why are there repeated values for them?

Thanks again

[vibansal]

looks like there were 0 markers shared between the input file and the reference allele frequency panel. Please check if there are shared markers and the input format is correct.

[PhilPalmer]

Hi @vibansal,

Ah okay, thank you very much for the prompt response.

I am just using a 23andMe file which I converted to plink format using 23andme-to-plink and plink

The reference file was downloaded from here and I was using the wrong one before

I now get the following output & the two output files produced:

$ python ancestry/runancestry.py --plink 23andMe/uk35C650_20170608144013 -f k27.iadmix -o test --path /ancestry/
reading allele frequency file k27.iadmix
reading mapfile 23andMe/uk35C650_20170608144013.map


ancestry admixture calculations for individual: 1 uk35C650_20170608144013 using 72100 markers
contribution of ancestry from pop Amerindian is not significant: delta 0.019042 admixture_prop 0.003104
contribution of ancestry from pop Uralic is not significant: delta 0.231992 admixture_prop 0.006480
contribution of ancestry from pop Centralasian is not significant: delta 3.353051 admixture_prop 0.017833
contribution of ancestry from pop Northindian is not significant: delta 4.545982 admixture_prop 0.026220

final maxval -57516.357045 ADMIX_PROP AHG:0.000000 Amerindian:0.000000 Arctic:0.000000 ASI:0.000000 Australomelanesian:0.000000 Austronesian:0.000000 Baltic:0.270832 Caucasian:0.073557 Centralasian:0.000000 EA:0.000000 Eastafrican:0.000000 Finnic:0.094336 NEA:0.115838 Northafrican:0.036541 Northeuropean:0.116998 Northindian:0.000000 Onge:0.000000 Paleosiberian:0.000000 Pygmy:0.000000 Sahul:0.000000 SEA:0.000000 Siberian:0.000000 Southeuropean:0.198954 SSA:0.000000 Uralic:0.000000 Westafrican:0.000000 Westasian:0.092945
AHG:0.0000:0.00 Amerindian:0.0000:0.02 Arctic:0.0000:0.00 ASI:0.0000:0.00 Australomelanesian:0.0000:0.00 Austronesian:0.0000:0.00 Baltic:0.2708:203.50 Caucasian:0.0736:15.99 Centralasian:0.0000:3.35 EA:0.0000:0.00 Eastafrican:0.0000:0.00 Finnic:0.0943:43.65 NEA:0.1158:46.11 Northafrican:0.0365:10.41 Northeuropean:0.1170:78.78 Northindian:0.0000:4.55 Onge:0.0000:0.00 Paleosiberian:0.0000:0.00 Pygmy:0.0000:0.00 Sahul:0.0000:0.00 SEA:0.0000:0.00 Siberian:0.0000:0.00 Southeuropean:0.1990:190.39 SSA:0.0000:0.00 Uralic:0.0000:0.23 Westafrican:0.0000:0.00 Westasian:0.0929:24.91 FINAL_ALL_PROPS
Baltic:0.2708:203.50 Caucasian:0.0736:15.99 Finnic:0.0943:43.65 NEA:0.1158:46.11 Northafrican:0.0365:10.41 Northeuropean:0.1170:78.78 Southeuropean:0.1990:190.39 Westasian:0.0929:24.91 FINAL_NZ_PROPS bins 200 ssq 9.677811
LL -57516.357045 LL_exp -57490.292080 146.429183 0.999

Does this look correct now as there are now 72100 markers?
How do I interpret the output?

Thanks