[Problem opening file: '-fold'] --> angst-wrapper SFS ./Site_Frequency_Spectrum_Config in online tutorial about angsd-wrapper HOT 4 OPEN

/mnt/steelhead/remote/Sophie/scratch/Maize/SFS$ /mnt/steelhead/remote/Sophie/Programs/angsd-wrapper/dependencies/angsd/misc/realSFS ./Maize_SFSOut.saf.idx
        -> Version of fname:./Maize_SFSOut.saf.idx is:2
        -> Assuming .saf.gz file: ./Maize_SFSOut.saf.gz
        -> Assuming .saf.pos.gz: ./Maize_SFSOut.saf.pos.gz
        -> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fname:./Maize_SFSOut.saf.idx fstout:(null) oldout:0 seed:1635892830 bootstrap:0
        -> You are printing the optimized SFS to the terminal consider dumping into a file
        -> E.g.: './realSFS ./Maize_SFSOut.saf.idx >sfs.ml.txt'
        -> nSites: 873481
        -> The choice of -nSites will require atleast: 83.301636 megabyte memory, that is at least: 1.05% of total memory
        -> dim(./Maize_SFSOut.saf.idx):23
        -> Dimension of parameter space: 23
        -> Done reading data from chromosome will prepare next chromosome
        -> Is in multi sfs, will now read data from chr:10
        -> 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
        -> Will run optimization on nSites: 873481
------------
startlik=-3393452.567606
lik[2]=-225047.521432 diff=3.168405e+06 alpha:1.000000 sr2:9.277772e-01
lik[5]=-225010.243117 diff=3.727831e+01 alpha:1.284184 sr2:1.180093e-07
lik[8]=-225008.303606 diff=1.939511e+00 alpha:3.949081 sr2:1.254134e-09
lik[11]=-225008.300234 diff=3.372127e-03 alpha:1.904168 sr2:4.637274e-12
        -> Breaking EM(sr2) at iter:12, sqrt(sr2):2.292394e-07
likelihood: -225008.300234
------------
837794.500918 0.000000 5871.665062 0.000000 3235.764685 0.000000 1832.887050 0.000000 1379.652548 0.000000 1391.708114 0.000000 1219.220259 0.000000 938.974705 0.000000 881.494241 0.000000 1172.368006 0.000000 1678.848464 0.000000 16083.915949
        -> Only read nSites: 0 will therefore prepare next chromosome (or exit)

        -> NB 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))

-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
	-> NB 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))

-> angsd version: 0.911-44-g1c0ebb6 (htslib: 1.3.1-30-gbb03b02) build(Sep 14 2022 09:44:04)
-> Reading fasta: /gpfs/group/restricted/drc9/restricted/Lan/dotfiles/angsd-wrapper/Example_Data/Sequences/Tripsacum_TDD39103.fa
-> Reading fasta: /gpfs/group/restricted/drc9/restricted/Lan/dotfiles/angsd-wrapper/Example_Data/Sequences/Zea_mays.AGPv3.30.dna_sm.chromosome.10.fa
-> (Using Filipe G Vieira modification of: abcSaf.cpp)
-> Parsing 11 number of samples
-> Region lookup 1/1

-> We have now allocated approximately 10 Megabytes of raw nodes to the nodepool

-> We have now allocated approximately 20 Megabytes of raw nodes to the nodepool
-> Printing at chr: 10 pos:15302669 chunknumber 100
-> Printing at chr: 10 pos:15780341 chunknumber 200
-> Printing at chr: 10 pos:16322598 chunknumber 300
-> Printing at chr: 10 pos:16492300 chunknumber 400
-> Printing at chr: 10 pos:16660947 chunknumber 500
-> Printing at chr: 10 pos:16771873 chunknumber 600
-> Printing at chr: 10 pos:16943362 chunknumber 700
-> Printing at chr: 10 pos:17114919 chunknumber 800
-> Printing at chr: 10 pos:17264910 chunknumber 900
-> Printing at chr: 10 pos:17405281 chunknumber 1000
-> Printing at chr: 10 pos:17551496 chunknumber 1100
-> Printing at chr: 10 pos:17759315 chunknumber 1200
-> Printing at chr: 10 pos:17906277 chunknumber 1300
-> Printing at chr: 10 pos:18074909 chunknumber 1400
-> Printing at chr: 10 pos:18231910 chunknumber 1500
-> Printing at chr: 10 pos:18354120 chunknumber 1600
-> Printing at chr: 10 pos:18713498 chunknumber 1700
-> Printing at chr: 10 pos:18966706 chunknumber 1800
-> Printing at chr: 10 pos:19170751 chunknumber 1900
-> Printing at chr: 10 pos:19386992 chunknumber 2000

-> Done reading data waiting for calculations to finish
-> Done waiting for threads

-> npools:27 unfreed tnodes before clean:0
-> Output filenames:
	->"/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.arg"
	->"/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.mafs.gz"
	->"/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.geno.gz"
	->"/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.saf.gz"
	->"/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.saf.pos.gz"
	->"/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.saf.idx"
-> Wed Sep 14 17:12:37 2022
-> Arguments and parameters for all analysis are located in .arg file
[ALL done] cpu-time used =  344.06 sec
[ALL done] walltime used =  217.00 sec
-> Version of fname:/gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.saf.idx is:2
-> Assuming .saf.gz file: /gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.saf.gz
-> Assuming .saf.pos.gz: /gpfs/scratch/lxw34/lowCov/angsd_wrapper/Maize/SFS/Maize_SFSOut.saf.pos.gz
-> Problem opening file: '-fold'