Re: [scipion-users] Exporting the particles from cryospar to SCIPION

[Roberto M. <ro...@cn...>]

Furthermore, MRC is a tricky format that has been expanded by different
packages  and reimplemented several times so there are several dialects.
Scipion tries to honor the definition described here:

MRC2014: Extensions to the MRC format header for electron cryo-microscopy
and tomography
Journal of Structural Biology 192.2 (2015): 146-150

I do not know about cryosparc

     Roberto

On Tue, May 18, 2021 at 2:19 PM Pablo Conesa <pc...@cn...> wrote:

> I'd say there is a error in the association of the image files.
>
> readMRC: Image number 11 exceeds stack size 1 of image 000011@Runs/001300_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
>
> Basically,
> 024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
> does not have 11 images?
>
>
> On 18/5/21 12:34, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
> We managed to import the particles from cryosparc into SCIPION (thanks to Grigory)
>
> But when I want to run the 2D classification I get the error:
>
>
> 1. With relion
>
>
>
> Follower     2 runs on host            = cryoem01
> 00031:    =================
> 00032:    uniqueHost cryoem01 has 2 ranks.
> 00033:   GPU-ids not specified for this rank, threads will automatically be mapped to available devices.
> 00034:    Thread 0 on follower 1 mapped to device 0
> 00035:    Thread 1 on follower 1 mapped to device 0
> 00036:    Thread 2 on follower 1 mapped to device 0
> 00037:   GPU-ids not specified for this rank, threads will automatically be mapped to available devices.
> 00038:    Thread 0 on follower 2 mapped to device 1
> 00039:    Thread 1 on follower 2 mapped to device 1
> 00040:    Thread 2 on follower 2 mapped to device 1
> 00041:    Running CPU instructions in double precision.
> 00042:    + WARNING: Changing psi sampling rate (before oversampling) to 5.625 degrees, for more efficient GPU calculations
> 00043:    + On host cryoem01: free scratch space = 448.912 Gb.
> 00044:    Copying particles to scratch directory: /data1/new_scratch/relion_volatile/
> 00045:   000/??? sec ~~(,_,">                                                          [oo]
> 00046:      0/   0 sec ~~(,_,">in: /opt/Scipion3/software/em/relion-3.1.2/src/rwMRC.h, line 192
> 00047:   ERROR:
> 00048:   readMRC: Image number 11 exceeds stack size 1 of image 000011@Runs/001300_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
> 00049:   === Backtrace  ===
> 00050:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x4786a1]
> 00051:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0x99f) [0x4b210f]
> 00052:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x17b) [0x4b407b]
> 00053:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN10Experiment22copyParticlesToScratchEibbd+0xda7) [0x5b8f87]
> 00054:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x210) [0x498540]
> 00055:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9aa) [0x49ab2a]
> 00056:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(main+0x55) [0x4322a5]
> 00057:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f219de79555]
> 00058:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi() [0x435fbf]
> 00059:   ==================
> 00060:   ERROR:
> 00061:   readMRC: Image number 11 exceeds stack size 1 of image 000011@Runs/001300_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
> 00062:   application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> 00063:   Traceback (most recent call last):
> 00064:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
> 00065:       self._run()
> 00066:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run
> 00067:       resultFiles = self._runFunc()
> 00068:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc
> 00069:       return self._func(*self._args)
> 00070:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py", line 811, in runRelionStep
> 00071:       self.runJob(self._getProgram(), params)
> 00072:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
> 00073:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
> 00074:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
> 00075:       process.runJob(log, programName, params,
> 00076:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
> 00077:       return runCommand(command, env, cwd)
> 00078:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
> 00079:       check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
> 00080:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
> 00081:       raise CalledProcessError(retcode, cmd)
> 00082:   subprocess.CalledProcessError: Command ' mpirun -np 3  `which relion_refine_mpi` --i Runs/001300_ProtRelionClassify2D/input_particles.star --particle_diameter 690 --zero_mask  --K 64 --norm  --scale  --o Runs/001300_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3' returned non-zero exit status 1.
> 00083:   Protocol failed: Command ' mpirun -np 3  `which relion_refine_mpi` --i Runs/001300_ProtRelionClassify2D/input_particles.star --particle_diameter 690 --zero_mask  --K 64 --norm  --scale  --o Runs/001300_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3' returned non-zero exit status 1.
> 00084:   FAILED: runRelionStep, step 2, time 2021-05-18 12:25:42.553565
> 00085:   *** Last status is failed
> 00086:   ------------------- PROTOCOL FAILED (DONE 2/3)
>
>
>
> 2. With cryosparc
>
> — no CTF information.
>
>
> Could you please suggest the solution?
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
>
> _______________________________________________
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>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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