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KHanghoj / NGSremix

GNU General Public License v2.0
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-nan values only for k0 k1 k2 #8

Open fuesseler opened 3 months ago

fuesseler commented 3 months ago

Hello!

Thanks for developing this tool! Unfortunately, my results only consist of -nan entries and I am not sure why:

ind1 ind2 k0 k1 k2 nIter 1 2 -nan -nan -nan 4999 1 3 -nan -nan -nan 4999 1 4 -nan -nan -nan 4999 etc.

First few lines of hte anccoef file look like this

nd paired_est paired_iter paired_ll parental_est parental_iter parental_ll 1 0.000009,0.000015,0.000025,0.000017,0.000000,0.000000,0.000000,0.000017,0.000013,0.000000,0.000000,0.000002,0.000024,0.000000,0.000000,0.000006,0.000000,0.000000,0.999290,0.000582,0.000000 20 -63875.961217 0.000001,0.000001,0.000001,0.000001,0.999996,0.000001,0.000001,0.000001,0.000001,0.000001,0.999996,0.000001 23 -63872.212146 2 0.000008,0.000018,0.000029,0.000022,0.000000,0.000000,0.000000,0.000017,0.000015,0.000000,0.000000,0.000002,0.000027,0.000000,0.000000,0.000006,0.000000,0.000000,0.999109,0.000746,0.000000 20 -63659.846986 0.000001,0.000001,0.000001,0.000001,0.999996,0.000001,0.000001,0.000001,0.000005,0.000001,0.999991,0.000001 23 -63655.405118

This is the log output:

/work/uesseler/software/NGSremix/src/NGSremix -beagle merged_minInd90_gdfilter_unlinked150kbr01.beagle.gz -qname results/WEIRexcl_ngsLD_150kb/6/admixResult.6.57.qopt -fname results/WEIRexcl_ngsLD_150kb/6/admixResult.6.57.fopt.gz -seed 1 -o ngsremix_K6_res -P 32 -> Seed is: 1 -> Beagle - Reading from: merged_minInd90_gdfilter_unlinked150kbr01.beagle.gz -> Beagle - 135843 sites and 30 nInd processed -> Beagle - Transpose from 135843 X 303 to 30 X 1358433 -> K=6 nSites=135843 nInd=30 -> Opening : results/WEIRexcl_ngsLD_150kb/6/admixResult.6.57.fopt.gz with x=135843 y=6 -> Estimating ancestry coefficients. Dumping to ngsremix_K6_res.anccoef -> 30 ancestry estimates took 5 sec. [ALL done] cpu-time used = 4108.21 sec [ALL done] walltime used = 147.00 sec [ALL done] results have been outputted to ngsremix_K6_res

I tried using this script ( https://github.com/KHanghoj/maf_beagle_ngsadmix ) but it doesn't remove anything from my Beagle file ( I suppose because that already has -minMaf 0.05 incorporated from the beginning). Do you have any ideas what might be going wrong?

Banthandor commented 5 days ago

I have the same issue, did you manage to solve it?

fuesseler commented 5 days ago

Unfortunately not. I'd still be interested in a solution.

KHanghoj commented 4 days ago

Hi.

Sorry for the late reply.

Have you tried to use the latest release?

On Thu, Sep 12, 2024 at 2:03 PM FU @.***> wrote:

Reopened #8 https://github.com/KHanghoj/NGSremix/issues/8.

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