Hello,
By using the parameter setting below, I am trying to obtain the results for further analysis in Structure harvester. However, even tough I check the option "compute the probability of the data (for estimating K)", I cannot find the related result file in any folders related to the analysis. But my input file is correct, the analysis runs without problem and I obtain the result files on correct folders, the only problem is missing file to use in structure harvester, which should be named for example "K1ReRun_run_1_f". What am I missing? If you make some suggestions I will be appreciated.
Length of Burnin Period: 10000
Number of MCMC Reps after Burnin: 50000
Ancestry Model Info: No Admixture Model
* Use Sampling Location Information
* Use Population IDs as Sampling Location Information
Frequency Model Info: Allele Frequencies are Correlated among Pops
* Assume Different Values of Fst for Different Subpopulations
* Prior Mean of Fst for Pops: 0.01
* Prior SD of Fst for Pops: 0.05
* Use Constant Lambda (Allele Frequencies Parameter)
* Value of Lambda: 1.0
Advanced Options
Estimate the Probability of the Data Under the Model
Frequency of Metropolis update for Q: 10
and I tried the same with different iteration numbers: 1, 5, 10
Thank you for your reply! So what I mean, in the results file I have only "turkey4_no_admix_corr_run_1_f" named files, when I try to use harvester, I get this message "Error string: StructureHarvester: In file admix_corr_10-50Resultsadmix_corr_10-50_run_5_f, unable to read value for k This can be caused by forgetting to check the box "Compute the probability of the data (for estimating K)" in STRUCTURE.". But I checked that box.
When I check the example file on the harvester web page there are 33 "Admix_run_033_f" files and only 3 "K1ReRun_run_3_f" files. When I say I obtain results I mean, the software completes the job and gives me results that I can plot. But without K file which I need for harvester. For the replicates, I used the lowest but it is just to see if it is working or not.
I followed the instructions, including harvester's. Thé file name that I wrote is just the first one , since the job completed I have the all files for each repeat. I will try to find another way thank you.
How many files did you end up getting per K value? Make sure this matches with the number of replicates you specified. I've had problems with the GUI version of Structure not producing the correct number of replicates for each K value before. You might consider posting a .zip archive of your files so they can be inspected
Thank you for your reply, I really did not understand what was the problem with first simulations that I tried with different values, but the new ones are working. Maybe there was a temporary problem, I really don't know. For now, I get results from harvester.
Edit: It might sound unrelated, but it might be because of a virus was interfering with softwares. Because also geneclass2 was not working, after I deleted a suspicious file they both started to work.
Thanks a lot again!
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