"No genotype data exists" when trying to run Populations
Cecilia Hjort
Logging to '/proj/snic2022-22-51/populations/ADMIXTURE/populations.log'.
Locus/sample distributions will be written to '/proj/snic2022-22-51/populations/ADMIXTURE/populations.log.distribs'.
populations parameters selected:
Percent samples limit per population: 0
Locus Population limit: 1
Percent samples overall: 0.8
Minor allele frequency cutoff: 0.03
Maximum observed heterozygosity cutoff: 1
Applying Fst correction: P-value correction.
Pi/Fis kernel smoothing: off
F-stats kernel smoothing: off
Bootstrap resampling: off
Parsing population map...
The population map contained 188 samples, 16 population(s), 1 group(s).
Warning: No genotype data exists for 188 of the samples listed in the population map.
Error: No more samples.
Aborted.
I've attached the gstacks.log file and the ref_map.log file from running the ref_map.pl script to generate the catalog.fa.gz.
The populations script I'm trying to run is:
populations -P /proj/snic2022-22-51/process_radtags/samples/aligned_reads -M /proj/snic2022-22-51/metadata/popmap_bombus_nooutliers -R 0.80 --min-maf 0.03 --min-mac 2 --hwe --vcf --structure --genepop --plink --fstats --fst-correction --p-value-cutoff --write-single-snp --ordered-export -t 4 -O /proj/snic2022-22-51/populations/ADMIXTURE
The popmap has the samples listed with the same suffix as the bam files in the /aligned_reads folder.
//Cilla
Catchen, Julian
Hi,
The populations program ran successfully on your data set as part of the refmap.pl run, so that would imply that you have done something different/incorrect in your current population map (popmap_bombus_nooutliers) versus the original one (popmap_bombus_all).
julian