I'm trying to identify SNP outliers on my GBS (genotype-by-sequencing) SNP dataset. I found "Arlequin" and have installed it successfully. Furthermore, I've converted my "VCF" file into "arp" which is the format needed for Arlequin. When I load my data into Arlequin and choose "Detecting loci under selection" and press "Start", I don't get any results. This is the error I get:
Any idea what the problem is? Is there any other software I can use to identify GBS SNP outliers? Thank you.
Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (09/02/23 at 10:25:07) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Impossible to detect outlier loci when no genetic structure is defined //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (09/02/23 at 10:25:07)) Total computing time for this run : 0h 0m 0s 851 ms //////////////////////////////////////////////////////////////////// Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (09/02/23 at 10:31:11) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Impossible to detect outlier loci when no genetic structure is defined //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (09/02/23 at 10:31:12)) Total computing time for this run : 0h 0m 0s 998 ms //////////////////////////////////////////////////////////////////// Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (09/02/23 at 10:32:42) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Impossible to detect outlier loci when no genetic structure is defined //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (09/02/23 at 10:32:43)) Total computing time for this run : 0h 0m 0s 965 ms //////////////////////////////////////////////////////////////////// Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (10/02/23 at 14:38:45) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Observed F-statistics lead to invalid migration rates. Coalescent simulations cannot be performed. Perform a simple AMOVA to check that all F-statistics are within the interval ]0..1[ //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (10/02/23 at 14:38:46)) Total computing time for this run : 0h 0m 1s 117 ms //////////////////////////////////////////////////////////////////// Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (10/02/23 at 14:52:56) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Observed F-statistics lead to invalid migration rates. Coalescent simulations cannot be performed. Perform a simple AMOVA to check that all F-statistics are within the interval ]0..1[ //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (10/02/23 at 14:52:57)) Total computing time for this run : 0h 0m 0s 755 ms //////////////////////////////////////////////////////////////////// Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (10/02/23 at 15:14:39) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- Analysis of Molecular Variance: ------------------------------- No. of Permutations = 1000 Distance matrix: Compute distance matrix Molecular distance : Pairwise difference Gamma a value = 0 #[WARNING # 1] : invalid structure: only one population per group An AMOVA analysis was selected and no Genetic structure is defined, AMOVA task is skipped. ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Observed F-statistics lead to invalid migration rates. Coalescent simulations cannot be performed. Perform a simple AMOVA to check that all F-statistics are within the interval ]0..1[ //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (10/02/23 at 15:14:40)) Total computing time for this run : 0h 0m 0s 739 ms //////////////////////////////////////////////////////////////////// Arlequin results //////////////////////////////////////////////////////////////////// RUN NUMBER 1 (10/02/23 at 15:22:49) //////////////////////////////////////////////////////////////////// Project information: -------------------- NbSamples = 3 DataType = DNA GenotypicData = 1 GameticPhase = 0 RecessiveData = 0 ============================== Settings used for Calculations ============================== General settings: ----------------- Deletion Weight = 1 Transition Weight Weight = 1 Tranversion Weight Weight = 1 Epsilon Value = 1e-007 Significant digits for output = 5 Use original haplotype definition Alllowed level of missing data = 0.05 Active Tasks: ------------- ============================================================================== == DETECTION OF LOCI UNDER SELECTION FROM GENOME SCANS BASED ON F-STATISTICS ============================================================================== Beaumont, M.A., and Nichols, R.A., 1996. Excoffier, L. Hofer, T. and Foll,M. 2009. Observed F-statistics lead to invalid migration rates. Coalescent simulations cannot be performed. Perform a simple AMOVA to check that all F-statistics are within the interval ]0..1[ //////////////////////////////////////////////////////////////////// END OF RUN NUMBER 1 (10/02/23 at 15:22:49)) Total computing time for this run : 0h 0m 0s 761 ms ////////////////////////////////////////////////////////////////////
Is Arlequin right that you have 3 samples? In that case, I don't think you can easily detect signatures for selection.
Well, it's quite confusing because it recognizes samples as populations. I have three populations, that for whatever reason are labeled as samples. Within each population, or sample, I have 6 - 7 "samples".
This suggests some problem in the definition of individuals and populations. You may check the structure of your files against that of Arlequin example files (included in the distribution) and see if you can get an idea of what is going on. I used to start from the example files and fill them with my data to be sure that the structure was correct.
I have done precisely that, and according to the manual, my setup looks like it theirs.