start 2026-09-28T08:51:13Z host n3465 pair=NS18_Disco_Wild__Squaxin_Island [persaf::persaf_init] Version of output/06_angsd_structure/saf/NS18_Disco_Wild.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/NS18_Disco_Wild.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/NS18_Disco_Wild.saf.pos.gz [persaf::persaf_init] Version of output/06_angsd_structure/saf/Squaxin_Island.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/Squaxin_Island.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/Squaxin_Island.saf.pos.gz -> args: tole:0.000000 nthreads:16 maxiter:60 nsites(block):0 start:(null) chr:CM196826.1 start:-1 stop:-1 fstout:(null) oldout:0 seed:-1 bootstrap:0 resample_chr:0 whichFst:0 fold:1 ref:(null) anc:(null) [main] Multi SFS is 'still' under development. Please report strange behaviour. -> The choice of -nSites will require atleast: 7558.871582 megabyte memory, that is at least: 0.49% of total memory -> dim(output/06_angsd_structure/saf/NS18_Disco_Wild.saf.idx):17 -> dim(output/06_angsd_structure/saf/Squaxin_Island.saf.idx):15 -> Dimension of parameter space: 255 -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196826.1] from pop0: 80407931 -> Sites to keep[CM196826.1] from pop1: 80407931 -> Will run optimization on nSites: 80407931 ------------ startlik=-373057952.880193 -> Instability detected, accelerated guess is too close to bound or outside will fallback to regular EM for this step likelihood: -10244744.445754 ------------ -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> NB output is no longer log probs of the frequency spectrum! -> Output is now simply the expected values! -> You can convert to the old format simply with log(norm(x)) -> Please check that it has converged! -> You can add start new optimization by supplying -sfs FILE, where is >FILE from this run -> -maxIter INT -tole FLOAT [persaf::persaf_init] Version of output/06_angsd_structure/saf/NS18_Disco_Wild.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/NS18_Disco_Wild.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/NS18_Disco_Wild.saf.pos.gz [persaf::persaf_init] Version of output/06_angsd_structure/saf/Squaxin_Island.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/Squaxin_Island.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/Squaxin_Island.saf.pos.gz -> args: tole:0.000000 nthreads:16 maxiter:100 nsites(block):0 start:output/06_angsd_structure/fst/NS18_Disco_Wild__Squaxin_Island.ml chr:(null) start:-1 stop:-1 fstout:output/06_angsd_structure/fst/NS18_Disco_Wild__Squaxin_Island oldout:0 seed:-1 bootstrap:0 resample_chr:0 whichFst:0 fold:1 ref:(null) anc:(null) -> nSites: 100000 -> IMPORTANT: please make sure that your saf files haven't been folded with -fold 1 in -doSaf in angsd -> [reynoldFst] sfs1:16 sfs2:14 dimspace:255 -> generating offset remapper lookup -> Reading: output/06_angsd_structure/fst/NS18_Disco_Wild__Squaxin_Island.ml assuming counts (will normalize to probs internally) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196826.1] from pop0: 80407931 -> Sites to keep[CM196826.1] from pop1: 80407931 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196827.1] from pop0: 80011972 -> Sites to keep[CM196827.1] from pop1: 80011972 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196828.1] from pop0: 79216980 -> Sites to keep[CM196828.1] from pop1: 79216980 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196829.1] from pop0: 69276681 -> Sites to keep[CM196829.1] from pop1: 69276681 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196830.1] from pop0: 69115537 -> Sites to keep[CM196830.1] from pop1: 69115537 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196831.1] from pop0: 42329332 -> Sites to keep[CM196831.1] from pop1: 42329332 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196832.1] from pop0: 55007354 -> Sites to keep[CM196832.1] from pop1: 55007354 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196833.1] from pop0: 45244645 -> Sites to keep[CM196833.1] from pop1: 45244645 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196834.1] from pop0: 31541065 -> Sites to keep[CM196834.1] from pop1: 31541065 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> Done reading data from chromosome will prepare next chromosome -> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect -> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites -> Sites to keep[CM196835.1] from pop0: 29005474 -> Sites to keep[CM196835.1] from pop1: 29005474 -> Only read nSites: 0 will therefore prepare next chromosome (or exit) -> fst index finished with no errors! Example runs: realSFS fst stats output/06_angsd_structure/fst/NS18_Disco_Wild__Squaxin_Island.fst.idx realSFS fst stats2 output/06_angsd_structure/fst/NS18_Disco_Wild__Squaxin_Island.fst.idx end 2026-09-28T09:59:34Z pair=NS18_Disco_Wild__Squaxin_Island fst=0.031604 0.049730