[scipion-users] Error running relion

[Dmitry S. <Sem...@gm...>]

Dear Grigory & colleagues,

Error running updated relion plugin. 


Any ideas?

Thank you

Sincerely,
Dmitry




File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001:   Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr
00002:   RUNNING PROTOCOL -----------------
00003:   Protocol starts
00004:   Hostname: localhost4.localdomain4
00005:   PID: 99422
00006:   pyworkflow: 3.0.17
00007:   plugin: relion
00008:   plugin v: 4.0b2
00009:   currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI
00010:   workingDir: Runs/004970_ProtRelionClassify2D
00011:   runMode: Continue
00012:             MPI: 6
00013:         threads: 4
00014:    Starting at step: 1
00015:    Running steps 
00016:   STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805
00017:   Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star'
00018:   convertBinaryFiles: creating soft links.
00019:      Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra
00020:   FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397
00021:   STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078
00022:    mpirun -np 6  `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf  --zero_mask  --K 24 --norm  --scale  --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc  --pool 3 --gpu   --j 4
00023:   Protocol failed: Command ' mpirun -np 6  `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf  --zero_mask  --K 24 --norm  --scale  --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc  --pool 3 --gpu   --j 4' returned non-zero exit status 213.
00024:   FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854
00025:   *** Last status is failed 
00026:   ------------------- PROTOCOL FAILED (DONE 2/3)