start 2026-09-28T06:27:13Z host n3477 pair=Dogfish_Bay__SS18_North_Bay_Wild [persaf::persaf_init] Version of output/06_angsd_structure/saf/Dogfish_Bay.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/Dogfish_Bay.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/Dogfish_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: 7643.163086 megabyte memory, that is at least: 0.49% of total memory -> dim(output/06_angsd_structure/saf/Dogfish_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: 80156707 -> Sites to keep[CM196826.1] from pop1: 80156707 -> Will run optimization on nSites: 80156707 ------------ startlik=-381125378.266013 -> Instability detected, accelerated guess is too close to bound or outside will fallback to regular EM for this step likelihood: -11147758.983054 ------------ -> 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/Dogfish_Bay.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/Dogfish_Bay.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/Dogfish_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/Dogfish_Bay__SS18_North_Bay_Wild.ml chr:(null) start:-1 stop:-1 fstout:output/06_angsd_structure/fst/Dogfish_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/Dogfish_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: 80156707 -> Sites to keep[CM196826.1] from pop1: 80156707 -> 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: 79398872 -> Sites to keep[CM196827.1] from pop1: 79398872 -> 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: 79101258 -> Sites to keep[CM196828.1] from pop1: 79101258 -> 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: 68868902 -> Sites to keep[CM196829.1] from pop1: 68868902 -> 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: 68930557 -> Sites to keep[CM196830.1] from pop1: 68930557 -> 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: 41697100 -> Sites to keep[CM196831.1] from pop1: 41697100 -> 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: 55130898 -> Sites to keep[CM196832.1] from pop1: 55130898 -> 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: 45470866 -> Sites to keep[CM196833.1] from pop1: 45470866 -> 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: 31210619 -> Sites to keep[CM196834.1] from pop1: 31210619 -> 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: 28951799 -> Sites to keep[CM196835.1] from pop1: 28951799 -> 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/Dogfish_Bay__SS18_North_Bay_Wild.fst.idx realSFS fst stats2 output/06_angsd_structure/fst/Dogfish_Bay__SS18_North_Bay_Wild.fst.idx end 2026-09-28T07:42:02Z pair=Dogfish_Bay__SS18_North_Bay_Wild fst=0.033899 0.038339