start 2026-09-28T07:31:16Z host n3435 pair=HC18_Triton_Wild__LS [persaf::persaf_init] Version of output/06_angsd_structure/saf/HC18_Triton_Wild.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/HC18_Triton_Wild.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/HC18_Triton_Wild.saf.pos.gz [persaf::persaf_init] Version of output/06_angsd_structure/saf/LS.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/LS.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/LS.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: 7782.762207 megabyte memory, that is at least: 0.50% of total memory -> dim(output/06_angsd_structure/saf/HC18_Triton_Wild.saf.idx):15 -> dim(output/06_angsd_structure/saf/LS.saf.idx):15 -> Dimension of parameter space: 225 -> 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: 78047030 -> Sites to keep[CM196826.1] from pop1: 78047030 -> Will run optimization on nSites: 78047030 ------------ startlik=-345325483.495987 -> Instability detected, accelerated guess is too close to bound or outside will fallback to regular EM for this step likelihood: -10658556.467939 ------------ -> 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/HC18_Triton_Wild.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/HC18_Triton_Wild.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/HC18_Triton_Wild.saf.pos.gz [persaf::persaf_init] Version of output/06_angsd_structure/saf/LS.saf.idx is 3 [persaf::persaf_init] Assuming .saf.gz file is output/06_angsd_structure/saf/LS.saf.gz [persaf::persaf_init] Assuming .saf.pos.gz file is output/06_angsd_structure/saf/LS.saf.pos.gz -> args: tole:0.000000 nthreads:16 maxiter:100 nsites(block):0 start:output/06_angsd_structure/fst/HC18_Triton_Wild__LS.ml chr:(null) start:-1 stop:-1 fstout:output/06_angsd_structure/fst/HC18_Triton_Wild__LS 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] sfs1:14 sfs2:14 dimspace:225 -> generating offset remapper lookup -> Reading: output/06_angsd_structure/fst/HC18_Triton_Wild__LS.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: 78047030 -> Sites to keep[CM196826.1] from pop1: 78047030 -> 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: 77471408 -> Sites to keep[CM196827.1] from pop1: 77471408 -> 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: 77418299 -> Sites to keep[CM196828.1] from pop1: 77418299 -> 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: 67089992 -> Sites to keep[CM196829.1] from pop1: 67089992 -> 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: 66859061 -> Sites to keep[CM196830.1] from pop1: 66859061 -> 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: 40443251 -> Sites to keep[CM196831.1] from pop1: 40443251 -> 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: 53215900 -> Sites to keep[CM196832.1] from pop1: 53215900 -> 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: 43766402 -> Sites to keep[CM196833.1] from pop1: 43766402 -> 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: 29699937 -> Sites to keep[CM196834.1] from pop1: 29699937 -> 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: 27991498 -> Sites to keep[CM196835.1] from pop1: 27991498 -> 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/HC18_Triton_Wild__LS.fst.idx realSFS fst stats2 output/06_angsd_structure/fst/HC18_Triton_Wild__LS.fst.idx end 2026-09-28T08:35:51Z pair=HC18_Triton_Wild__LS fst=0.041202 0.087885