start 2026-09-28T09:03:33Z host n3473 pair=Ostrich_Bay__SS18_North_Bay_Wild [persaf::persaf_init] Version of output/06_angsd_structure/saf/Ostrich_Bay.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/Ostrich_Bay.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/Ostrich_Bay.saf.pos.gz [persaf::persaf_init] Version of output/06_angsd_structure/saf/SS18_North_Bay_Wild.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/SS18_North_Bay_Wild.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/SS18_North_Bay_Wild.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: 7584.289551 megabyte memory, that is at least: 0.49% of total memory -> dim(output/06_angsd_structure/saf/Ostrich_Bay.saf.idx):17 -> dim(output/06_angsd_structure/saf/SS18_North_Bay_Wild.saf.idx):17 -> Dimension of parameter space: 289 -> 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: 80016772 -> Sites to keep[CM196826.1] from pop1: 80016772 -> Will run optimization on nSites: 80016772 ------------ startlik=-381429649.230059 -> Instability detected, accelerated guess is too close to bound or outside will fallback to regular EM for this step likelihood: -11176666.642714 ------------ -> 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/Ostrich_Bay.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/Ostrich_Bay.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/Ostrich_Bay.saf.pos.gz [persaf::persaf_init] Version of output/06_angsd_structure/saf/SS18_North_Bay_Wild.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/SS18_North_Bay_Wild.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/SS18_North_Bay_Wild.saf.pos.gz -> args: tole:0.000000 nthreads:16 maxiter:100 nsites(block):0 start:output/06_angsd_structure/fst/Ostrich_Bay__SS18_North_Bay_Wild.ml chr:(null) start:-1 stop:-1 fstout:output/06_angsd_structure/fst/Ostrich_Bay__SS18_North_Bay_Wild 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 sfs2:16 dimspace:289 -> generating offset remapper lookup -> Reading: output/06_angsd_structure/fst/Ostrich_Bay__SS18_North_Bay_Wild.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: 80016772 -> Sites to keep[CM196826.1] from pop1: 80016772 -> 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: 79429299 -> Sites to keep[CM196827.1] from pop1: 79429299 -> 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: 79286708 -> Sites to keep[CM196828.1] from pop1: 79286708 -> 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: 69086365 -> Sites to keep[CM196829.1] from pop1: 69086365 -> 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: 69001725 -> Sites to keep[CM196830.1] from pop1: 69001725 -> 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: 41981235 -> Sites to keep[CM196831.1] from pop1: 41981235 -> 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: 55412443 -> Sites to keep[CM196832.1] from pop1: 55412443 -> 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: 45807687 -> Sites to keep[CM196833.1] from pop1: 45807687 -> 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: 31490399 -> Sites to keep[CM196834.1] from pop1: 31490399 -> 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: 29193156 -> Sites to keep[CM196835.1] from pop1: 29193156 -> 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/Ostrich_Bay__SS18_North_Bay_Wild.fst.idx realSFS fst stats2 output/06_angsd_structure/fst/Ostrich_Bay__SS18_North_Bay_Wild.fst.idx end 2026-09-28T10:16:30Z pair=Ostrich_Bay__SS18_North_Bay_Wild fst=0.034114 0.043783