Hello,
I met an error causing the job Non-uniform Refinement failed with applying Defocus refinement and Global CtfRefinemnt around 6 iterations.
However, it was running in my previous jobs and other proteins.
I guess it is due to the problem in package Matplotlib during plotting.
This is a ~700kb protein, and the cryoSPARC version is 3.1.0.
I posted the related Traceback below, could anyone give me some tips to solve it?
Thank you.
Yu
**** handle exception rc
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:756: RuntimeWarning: invalid value encountered in arcsin
viewdirs_elevation.append( n.arcsin(viewdir[2]) )
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:756: RuntimeWarning: invalid value encountered in arcsin
viewdirs_elevation.append( n.arcsin(viewdir[2]) )
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:945: RuntimeWarning: invalid value encountered in true_divide
fsc_true = (fsc_t - fsc_n) / (1.0 - fsc_n)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:756: RuntimeWarning: invalid value encountered in arcsin
viewdirs_elevation.append( n.arcsin(viewdir[2]) )
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:945: RuntimeWarning: divide by zero encountered in true_divide
fsc_true = (fsc_t - fsc_n) / (1.0 - fsc_n)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:945: RuntimeWarning: invalid value encountered in true_divide
fsc_true = (fsc_t - fsc_n) / (1.0 - fsc_n)
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/sigproc.py:649: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
x = n.linalg.lstsq(w.reshape((-1,1))A, wb)[0]
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:285: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/plotutil.py:27: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later.
self._target(*self._args, **self._kwargs)
/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later.
self._target(*self._args, **self._kwargs)
/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later.
self._target(*self._args, **self._kwargs)
/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later.
self._target(*self._args, **self._kwargs)
/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later.
self._target(*self._args, **self._kwargs)
/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later.
self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/refine/newrun.py”, line 466, in cryosparc_compute.jobs.refine.newrun.run_homo_refine
set status to failed
========= main process now complete.
========= monitor process now complete.