MatplotlibDeprecationWarning: Passing non-integers as three-element position specification is deprecated since 3.3 and will be removed two minor releases later

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.

Are the warnings related to the failure? The traceback begins after the warnings. Have you seen the warnings on other jobs?

The MatplotlibDeprecationWarning only happens in the failed job.
Other warnings, eg. RuntimeWarning, and FutureWarning also happed on other successful jobs.