I was trying to run the new version 1.15.4 hoping it would not give me error messages regarding missing data mask files, but I now seem to have an issue with the format of my files when I run the smc++ estimate of cv function.
Traceback (most recent call last):
File "/sw/bioinfo/SMC++/1.15.4/rackham/bin/smc++", line 8, in
sys.exit(main())
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/frontend/console.py", line 28, in main
cmds[args.command].main(args)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/commands/estimate.py", line 47, in main
analysis = Analysis(args.data, args)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/analysis/analysis.py", line 57, in init
self.run(1)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/analysis/base.py", line 121, in run
self._optimizer.run(niter or self._niter)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/optimize/optimizers.py", line 176, in run
res = self._minimize(x0, coords)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/optimize/optimizers.py", line 108, in _minimize
res = scipy.optimize.minimize(self._f, x0z,
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/site-packages/scipy/optimize/_minimize.py", line 690, in minimize
res = _minimize_powell(fun, x0, args, callback, bounds, **options)
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/site-packages/scipy/optimize/_optimize.py", line 3254, in _minimize_powell
elif np.isnan(fval) or np.isnan(x).any():
TypeError: ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
The snc++ vcf2scm seems to be working without any error. Has anyone encountered this issue before?
Hi,
I was trying to run the new version 1.15.4 hoping it would not give me error messages regarding missing data mask files, but I now seem to have an issue with the format of my files when I run the smc++ estimate of cv function.
Traceback (most recent call last): File "/sw/bioinfo/SMC++/1.15.4/rackham/bin/smc++", line 8, in
sys.exit(main())
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/frontend/console.py", line 28, in main
cmds[args.command].main(args)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/commands/estimate.py", line 47, in main
analysis = Analysis(args.data, args)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/analysis/analysis.py", line 57, in init
self.run(1)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/analysis/base.py", line 121, in run
self._optimizer.run(niter or self._niter)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/optimize/optimizers.py", line 176, in run
res = self._minimize(x0, coords)
File "/sw/bioinfo/SMC++/1.15.4/rackham/venv/lib/python3.10/site-packages/smcpp/optimize/optimizers.py", line 108, in _minimize
res = scipy.optimize.minimize(self._f, x0z,
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/site-packages/scipy/optimize/_minimize.py", line 690, in minimize
res = _minimize_powell(fun, x0, args, callback, bounds, **options)
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/site-packages/scipy/optimize/_optimize.py", line 3254, in _minimize_powell
elif np.isnan(fval) or np.isnan(x).any():
TypeError: ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
The snc++ vcf2scm seems to be working without any error. Has anyone encountered this issue before?
Regards, Nic