Help with FST in Angsd-wrapper

[clairemerot]

I am trying to do Fst with Angsd-wrapper but I run into a problem.
"WRAPPER: realSFS 2dsfs...
-> Problem opening file: '/home/claire/Softwares/angsd-wrapper/Essai_20AA20AB20BB/Results/Essai20AA_20BB_C38/Fst/AA_Intergenic.saf.idx'
WRAPPER: realSFS fst prep...
-> Problem opening file: '/home/claire/Softwares/angsd-wrapper/Essai_20AA20AB20BB/Results/Essai20AA_20BB_C38/Fst/AA_Intergenic.saf.idx'
WRAPPER: estimating global fst...
-> Assuming idxname:/home/claire/Softwares/angsd-wrapper/Essai_20AA20AB20BB/Results/Essai20AA_20BB_C38/Fst/AA.BB.fst.idx
-> Problem opening file: '/home/claire/Softwares/angsd-wrapper/Essai_20AA20AB20BB/Results/Essai20AA_20BB_C38/Fst/AA.BB.fst.idx'
WRAPPER: estimating windowed fst...
-> Assuming idxname:/home/claire/Softwares/angsd-wrapper/Essai_20AA20AB20BB/Results/Essai20AA_20BB_C38/Fst/AA.BB.fst.idx
-> Problem opening file: '/home/claire/Softwares/angsd-wrapper/Essai_20AA20AB20BB/Results/Essai20AA_20BB_C38/Fst/AA.BB.fst.idx'"

I think it comes from an earlier error in which it tells me "inbreeding_20BB.indF' should contain 19 values, but has 20". It has 20, because (i check) file bam list also has 20 files.

If I change it to 19 in the indF, I have the error "Mismatch between number of samples and inbreeding coefficients".

Now, I have edited the Fst.sh to make it ignore the mismatch error and I am giving it 19 inbreeding coefficients (for 20 samples), which does not make sense but just to see. It runs.

Yet, we have another error (I am giving it a fasta ref with only one scaffold, the same indicated by regions).
"Sorting the regions file
Error in FUN(X[[i]], ...) : objet 'ordered.positions' introuvable"

I found a dirty alternative: running the 2DSFS with the other git branch works for SFS (ignoring the mismatch nb samples/nb of inbreegind coeffisients).This one is fine with using the region given. Yet, after calculating SFS, it does not manage to finish the FST because it lost the folder shared.pos.gz outside the FST folder.
Coming back to the main Fst git branch, ignoring the mismatch nb samples/nb of inbreegind coeffisients, we can now finish FST calculation because it reuses the SFS stored in the folder. Yet, I don't think this is a very nice way to do that and I wonder whether it uses 20 individuals or 19.

Could you help me?? What am I doing wrong?
Thanks a lot
Claire