start 2026-09-28T08:17:11Z host n3451 pair=MB__Ostrich_Bay [persaf::persaf_init] Version of output/06_angsd_structure/saf/MB.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/MB.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/MB.saf.pos.gz [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 -> 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: 7620.118164 megabyte memory, that is at least: 0.49% of total memory -> dim(output/06_angsd_structure/saf/MB.saf.idx):17 -> dim(output/06_angsd_structure/saf/Ostrich_Bay.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: 80698474 -> Sites to keep[CM196826.1] from pop1: 80698474 -> Will run optimization on nSites: 80698474 ------------ startlik=-385607506.696654 -> Instability detected, accelerated guess is too close to bound or outside will fallback to regular EM for this step likelihood: -9197108.169333 ------------ -> 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/MB.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/MB.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/MB.saf.pos.gz [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 -> args: tole:0.000000 nthreads:16 maxiter:100 nsites(block):0 start:output/06_angsd_structure/fst/MB__Ostrich_Bay.ml chr:(null) start:-1 stop:-1 fstout:output/06_angsd_structure/fst/MB__Ostrich_Bay 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/MB__Ostrich_Bay.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: 80698474 -> Sites to keep[CM196826.1] from pop1: 80698474 -> 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: 79634710 -> Sites to keep[CM196827.1] from pop1: 79634710 -> 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: 79387792 -> Sites to keep[CM196828.1] from pop1: 79387792 -> 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: 69235521 -> Sites to keep[CM196829.1] from pop1: 69235521 -> 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: 69291729 -> Sites to keep[CM196830.1] from pop1: 69291729 -> 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: 42201995 -> Sites to keep[CM196831.1] from pop1: 42201995 -> 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: 55143900 -> Sites to keep[CM196832.1] from pop1: 55143900 -> 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: 45979213 -> Sites to keep[CM196833.1] from pop1: 45979213 -> 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: 31576218 -> Sites to keep[CM196834.1] from pop1: 31576218 -> 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: 29348916 -> Sites to keep[CM196835.1] from pop1: 29348916 -> 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/MB__Ostrich_Bay.fst.idx realSFS fst stats2 output/06_angsd_structure/fst/MB__Ostrich_Bay.fst.idx end 2026-09-28T09:32:10Z pair=MB__Ostrich_Bay fst=0.035249 0.062077