squisquater
commented
3 years ago UPDATE: I think there is something wrong with my Maize_SFSOut.saf.idx file but I'm not sure what the issue is. Specifically "Only read nSites: 0 will therefore prepare next chromosome (or exit)"
I found some related threads that suggest filtering is too stringent but since this is all based on the angsd-wrapper tutorial that doesn't seem the likely culprit.
/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))
carte731
jrmandel
wul88
I followed the installation instructions and the tutorial instructions but am running into an error when I try to run the Site Frequency Spectrum.
angsd-wrapper SFS ./Site_Frequency_Spectrum_ConfigThis is my output and it appears it's failing when trying to find the file needed to fold (or not fold) the spectrum, but it can't.
Looking at the wrapper shell script (Site_Frequency_Spectrum.sh) it appears that is failing in the final section of the script in the middle of a series of pipes to the final file which does get output in my scratch directory, it's just empty.
I can also include my configuration file if helpful (Site_Frequency_Spectrum_Config) which also directs the script to another configuration file in the same directory (Common_Config), but I'm wondering whether anyone else has run into this error while trying to move through this tutorial before. I am trying to figure out if this is a file path issue or if the SFS is not running correctly and there is some other error in the output file I am not identifying correctly.