I have been trying to run the program NGSadmix (http://www.popgen.dk/software/index.php/NgsAdmix) using nine whole genome sequences. The program will run, however, the output in my .fopt.gz and .qopt files only contain -nan in both columns (running a k=2).
I made a beagle input file using the angsd program (v0.918) and this code: angsd -GL 1 -out genolike -doGlf 2 -doMajorMinor 1 -SNP_pval 1e-5 -doMaf 1 -bam bam.filelist
where the bam.filelist is a file listing the location of each of the sorted and indexed .bam files on a new line.
I am running NGSadmix with this code: ./NGSadmix -likes genolike.beagle.gz -K 2 -o outputadmix
This is the log file I receive: Input: lname=genolike.beagle.gz nPop=2, fname=(null) qname=(null) outfiles=outputadmix Setup: seed=1520867306 nThreads=1 method=1 Convergence: maxIter=2000 tol=0.000010 tolLike50=0.100000 dymBound=0 Filters: misTol=0.050000 minMaf=0.050000 minLrt=0.000000 minInd=0 Input file has dim: nsites=25438921 nind=9 Input file has dim (AFTER filtering): nsites=25438921 nind=9 [ALL done] cpu-time used = 40718.93 sec [ALL done] walltime used = 41370.00 sec best like = -nan after 2000 iterations
The .qopt output file contains this information: $head outputadmix.qopt -nan -nan -nan -nan -nan -nan ...
I've tried re-making the input file, but am consistently getting the same results. I have had a hard time trouble-shooting this issue because I am unclear as to why I'm seeing -nan as a result.
Any suggestions for how to solve this problem would be much appreciated.