FileNotFoundError: [Errno 2] No such file or directory: ‘Refine3D/job023/run_it010_3DFSC.mrc’

[fergusonscripps]

Hi we are using a SLURM job submission system that doesn't use conda environments.
We can see that the spisonet.py is running as we are getting the _external_reconstruct.star and .mrc files but for some reason, presumably after a signal that the last iteration is complete, the program is looking for the 3DFSC.mrc but it hasn't been generated not sure why?

set CUDA_VISIBLE_DEVICES=0,1,2,3
set CONDA_ENV=None
set ISONET_WHITENING=True
set ISONET_WHITENING_LOW=10
set ISONET_RETRAIN_EACH_ITER=True
set ISONET_BETA=0.5
set ISONET_ALPHA=1
set ISONET_START_HEALPIX=3
set ISONET_ACC_BATCHES=2
set ISONET_EPOCHS=5
set ISONET_KEEP_LOWRES=False
set ISONET_LOWPASS=True
set ISONET_ANGULAR_WHITEN=False
set ISONET_3DFSD=False
set ISONET_FSC_05=False
set ISONET_FSC_WEIGHTING=True
set ISONET_START_RESOLUTION=15.0
set ISONET_KEEP_LOWRES= True
healpix = 3
symmetry = C1
mask_file = cryosparc_P485_J854_008_volume_mask_refine.mrc
pixel size = 0.718
resolution at 0.5 and 0.143 are 4.324894 and 3.910808
real limit resolution to 3.910808
eval “$(conda shell.bash hook)” && conda activate None && spisonet.py whitening Refine3D/job023/run_it010_half1_class001_unfil.mrc -o Refine3D/job023/run_it010_half1_class001_unfil.mrc --mask cryosparc_P485_J854_008_volume_mask_refine.mrc --high_res 3.910808 --low_res 10
sh: conda: command not found
sh: conda: command not found
eval “$(conda shell.bash hook)” && conda activate None && spisonet.py combine_map Refine3D/job023/run_it000_half1_class001.mrc Refine3D/job023/run_it010_half1_class001_unfil.mrc Refine3D/job023/run_it010_half1_class001_unfil.mrc 20.0 --mask_file cryosparc_P485_J854_008_volume_mask_refine.mrc
sh: conda: command not found
sh: conda: command not found
eval “$(conda shell.bash hook)” && conda activate None && spisonet.py whitening Refine3D/job023/run_it010_half2_class001_unfil.mrc -o Refine3D/job023/run_it010_half2_class001_unfil.mrc --mask cryosparc_P485_J854_008_volume_mask_refine.mrc --high_res 3.910808 --low_res 10
sh: conda: command not found
sh: conda: command not found
eval “$(conda shell.bash hook)” && conda activate None && spisonet.py combine_map Refine3D/job023/run_it000_half2_class001.mrc Refine3D/job023/run_it010_half2_class001_unfil.mrc Refine3D/job023/run_it010_half2_class001_unfil.mrc 20.0 --mask_file cryosparc_P485_J854_008_volume_mask_refine.mrc
sh: conda: command not found
sh: conda: command not found
sh: conda: command not found
sh: conda: command not found
Traceback (most recent call last):
File “/opt/applications/spisonet/1.0/lib/python3.8/site-packages/spIsoNet/bin/relion_wrapper.py”, line 433, in
with mrcfile.open(fscn, ‘r’) as mrc:
File “/opt/applications/python/3.8.3/gnu/lib/python3.8/site-packages/mrcfile/load_functions.py”, line 138, in open
return NewMrc(name, mode=mode, permissive=permissive,
File “/opt/applications/python/3.8.3/gnu/lib/python3.8/site-packages/mrcfile/mrcfile.py”, line 108, in init
self._open_file(name)
File “/opt/applications/python/3.8.3/gnu/lib/python3.8/site-packages/mrcfile/mrcfile.py”, line 125, in _open_file
self._iostream = open(name, self._mode + ‘b’)
FileNotFoundError: [Errno 2] No such file or directory: ‘Refine3D/job023/run_it010_3DFSC.mrc’
in: /tmp/relion/src/backprojector.cpp, line 1283
ERROR:
ERROR: there was something wrong with system call: python /opt/applications/spisonet/1.0/lib/python3.8/site-packages/spIsoNet/bin/relion_wrapper.py Refine3D/job023/run_it010_half1_class001_external_reconstruct.star
=== Backtrace ===
/opt/applications/relion/4.0b1/cuda/arch_default/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x52baa1]
/opt/applications/relion/4.0b1/cuda/arch_default/bin/relion_refine_mpi(_ZN13BackProjector19externalReconstructER13MultidimArrayIdER8FileNameS2_S2_S2_S2_bdi+0x20f3) [0x678e53]
/opt/applications/relion/4.0b1/cuda/arch_default/bin/relion_refine_mpi(_ZN14MlOptimiserMpi12maximizationEv+0x1229) [0x4721c9]
/opt/applications/relion/4.0b1/cuda/arch_default/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x587) [0x475827]
/opt/applications/relion/4.0b1/cuda/arch_default/bin/relion_refine_mpi(main+0x5f) [0x43439f]
/usr/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f2c67014555]
/opt/applications/relion/4.0b1/cuda/arch_default/bin/relion_refine_mpi() [0x437f9f]

ERROR:
ERROR: there was something wrong with system call: python /opt/applications/spisonet/1.0/lib/python3.8/site-packages/spIsoNet/bin/relion_wrapper.py Refine3D/job023/run_it010_half1_class001_external_reconstruct.star
RELION version: 4.0-beta-1-commit-1d8333
exiting with an error ...
[nodea0705:10070] [[62108,0],0] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file util/show_help.c at line 501
done