Re: [scipion-users] Export particles from cryosparc

[Grigory S. <sha...@gm...>]

Thank you, Pablo! Indeed I never considered mrcs to have a single 2D
particle, which is entirely possible.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Wed, May 19, 2021 at 10:45 AM Pablo Conesa <pc...@cn...> wrote:

> Hi, we've found the issue.
>
> Although import particles (files mode) seemed correct....it wasn't for
> only those mrcs files having a single image. 30 of them.
>
> Removing them at import time worked and now relion 2d classification works
> as expected.
>
> We'll fix it.
>
>
> Cheers!
>
>
> On 19/5/21 10:56, Grigory Sharov wrote:
>
> Hi Dmitry,
>
> I'll try to reproduce the error when I get a chance
>
> On Wed, May 19, 2021, 09:41 Pablo Conesa <pc...@cn...> wrote:
>
>> I see, maybe we can arrange a tele conf to see in detail what is wrong.
>> I'll contact you.
>> On 19/5/21 10:26, Dmitry Semchonok wrote:
>>
>> Dear Pablo and Grigory,
>>
>>
>> Thank you!
>>
>> Yes, I am well aware of the fact that there is no info for the CTF etc :)
>>
>>
>> All I need is just a nice aligned 2D set of images (from the set I
>> imported)
>>
>> (Ideally I would like to have this set just from cryosparc but I have no
>> idea how to do that right away :) )
>>
>> Please see the log of relion
>>
>>
>>
>> RUNNING PROTOCOL -----------------
>> 00002:   Hostname: cryoem01
>> 00003:   PID: 36440
>> 00004:   pyworkflow: 3.0.13
>> 00005:   plugin: relion
>> 00006:   plugin v: 3.1.2
>> 00007:   currentDir: /data1/ScipionUserData/projects/Caro__helix
>> 00008:   workingDir: Runs/001735_ProtRelionClassify2D
>> 00009:   runMode: Continue
>> 00010:             MPI: 3
>> 00011:         threads: 3
>> 00012:    Starting at step: 1
>> 00013:    Running steps
>> 00014:   STARTED: convertInputStep, step 1, time 2021-05-18
>> 15:06:21.557294
>> 00015:   Converting set from
>> 'Runs/001662_ProtImportParticles/particles.sqlite' into
>> 'Runs/001735_ProtRelionClassify2D/input_particles.star'
>> 00016:   convertBinaryFiles: creating soft links.
>> 00017:      Root: Runs/001735_ProtRelionClassify2D/extra/input ->
>> Runs/001662_ProtImportParticles/extra
>> 00018:   FINISHED: convertInputStep, step 1, time 2021-05-18
>> 15:06:22.474076
>> 00019:   STARTED: runRelionStep, step 2, time 2021-05-18 15:06:22.502665
>> 00020:    mpirun -np 3  `which relion_refine_mpi` --i
>> Runs/001735_ProtRelionClassify2D/input_particles.star --particle_diameter
>> 690 --zero_mask  --K 64 --norm  --scale  --o
>> Runs/001735_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
>> 00021:   RELION version: 3.1.2
>> 00022:   Precision: BASE=double, CUDA-ACC=single
>> 00023:
>> 00024:    === RELION MPI setup ===
>> 00025:    + Number of MPI processes             = 3
>> 00026:    + Number of threads per MPI process   = 3
>> 00027:    + Total number of threads therefore   = 9
>> 00028:    + Leader  (0) runs on host            = cryoem01
>> 00029:    + Follower     1 runs on host            = cryoem01
>> 00030:    + 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 = 447.485 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/001735_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) [0x7fea6a54e555]
>> 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/001735_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/001735_ProtRelionClassify2D/input_particles.star --particle_diameter
>> 690 --zero_mask  --K 64 --norm  --scale  --o
>> Runs/001735_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/001735_ProtRelionClassify2D/input_particles.star --particle_diameter
>> 690 --zero_mask  --K 64 --norm  --scale  --o
>> Runs/001735_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 15:06:24.609548
>> 00085:   *** Last status is failed
>> 00086:   ------------------- PROTOCOL FAILED (DONE 2/3)
>>
>>
>> *Additionally,*
>>
>> So it seemed from the first look that there is some issue with the image
>> 11 — I delete the image 11 but the problem still remained.
>>
>>
>>
>>
>> *Optionally,*
>>
>> I believe that xmipp-2D should work but I did not try it yet.
>>
>> Thank you
>>
>> Sincerely,
>> Dmitry
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 19. May 2021, at 10:13, Pablo Conesa <pc...@cn...> wrote:
>>
>> Hi! So, I think Grigory is right, you've gone through  the import
>> particles "without metadata info" therefore you only have the images
>> without any alignment information.
>>
>>
>> In theory, 2d classification should work with this kind of import. Could
>> you please share the logs of one of the relion classification?
>> On 19/5/21 9:26, Dmitry Semchonok wrote:
>>
>> Dear Grigory,
>>
>>
>> I did nothing much, just tried to start relion 2D // or cryosparc.
>>
>>
>> The only thing I tried additionally since I could no proceed is to a)
>> change the box size; b) just resave the subset with the same number of
>> images.
>>
>>
>> Please see the image.
>>
>> <Screenshot 2021-05-19 at 09.23.41.png>
>>
>>
>>  Thank you
>>
>> Sincerely,
>>
>> Dmitry
>>
>>
>> On 18. May 2021, at 15:19, Grigory Sharov <sha...@gm...>
>> wrote:
>>
>> Hi,
>>
>> I imagine you have 624 micrographs, so particles are exported to mrc on a
>> mic basis. I see you used the "files" option to import mrcs particles into
>> Scipion.  This means the imported particles have no metadata except pixel
>> size you provided.
>>
>> What did you do with them after import?
>>
>> Best regards,
>> Grigory
>>
>>
>> --------------------------------------------------------------------------------
>> Grigory Sharov, Ph.D.
>>
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>> e-mail: gs...@mr...
>>
>>
>> On Tue, May 18, 2021 at 2:12 PM Dmitry Semchonok <Sem...@gm...>
>> wrote:
>>
>>> Dear Grigory,
>>>
>>> Yes I did that — the particles are looking fine.
>>>
>>>
>>> I guess the issue still comes from the fact that originally in cryosparc
>>> Export the stacks of particle were placed into 624 mrc. But the number of
>>> particles is about 44 818.  So even after the renaming and the export I see
>>> this in SCIPION export log
>>>
>>> <Screenshot 2021-05-18 at 15.09.11.png>
>>>
>>> What I guess may help is if I somehow combine all those files in 1 mrcs
>>> first and then add import them to SCIPION.
>>> Do you perhaps know how to do that?
>>>
>>> Thank you
>>>
>>> Sincerely,
>>> Dmitry
>>>
>>>
>>>
>>> On 18. May 2021, at 15:02, Grigory Sharov <sha...@gm...>
>>> wrote:
>>>
>>> Hi Dmitry,
>>>
>>> as the error states your star file points to a non-existing image in the
>>> mrcs stack.  You need to check first if you import from cryosparc with mrcs
>>> worked correctly (open / display particles) then trace all the steps you
>>> did before 2D classification.
>>>
>>> Best regards,
>>> Grigory
>>>
>>>
>>> --------------------------------------------------------------------------------
>>> Grigory Sharov, Ph.D.
>>>
>>> MRC Laboratory of Molecular Biology,
>>> Francis Crick Avenue,
>>> Cambridge Biomedical Campus,
>>> Cambridge CB2 0QH, UK.
>>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>>> e-mail: gs...@mr...
>>>
>>>
>>> On Tue, May 18, 2021 at 1:25 PM Dmitry Semchonok <Sem...@gm...>
>>> wrote:
>>>
>>>> Dear Pablo,
>>>>
>>>>
>>>> Thank you. I heard about this option. For that I guess the
>>>> https://pypi.org/project/cs2star/ needs to be installed.
>>>>
>>>>
>>>>
>>>>
>>>> In Cryosparc itself there is an option to export files. And then what
>>>> we get is the mrc files with different number of particles in each.
>>>>
>>>> It appeared to be possible to rename mrc —> to —>mrcs. Then SCIPION can
>>>> import those particles.
>>>>
>>>> Currently the problem is that not relion nor cryosparc can run these
>>>> particles.
>>>>
>>>>
>>>>
>>>>
>>>> Relion stops with error:
>>>>
>>>>
>>>> 00001:   RUNNING PROTOCOL -----------------
>>>> 00002:   Hostname: cryoem01
>>>> 00003:   PID: 46455
>>>> 00004:   pyworkflow: 3.0.13
>>>> 00005:   plugin: relion
>>>> 00006:   plugin v: 3.1.2
>>>> 00007:   currentDir: /data1/ScipionUserData/projects/Caro__helix
>>>> 00008:   workingDir: Runs/001546_ProtRelionClassify2D
>>>> 00009:   runMode: Continue
>>>> 00010:             MPI: 3
>>>> 00011:         threads: 3
>>>> 00012:    Starting at step: 1
>>>> 00013:    Running steps
>>>> 00014:   STARTED: convertInputStep, step 1, time 2021-05-18
>>>> 12:33:26.198123
>>>> 00015:   Converting set from
>>>> 'Runs/001492_ProtUserSubSet/particles.sqlite' into
>>>> 'Runs/001546_ProtRelionClassify2D/input_particles.star'
>>>> 00016:   convertBinaryFiles: creating soft links.
>>>> 00017:      Root: Runs/001546_ProtRelionClassify2D/extra/input ->
>>>> Runs/001057_ProtImportParticles/extra
>>>> 00018:   FINISHED: convertInputStep, step 1, time 2021-05-18
>>>> 12:33:27.117588
>>>> 00019:   STARTED: runRelionStep, step 2, time 2021-05-18 12:33:27.145974
>>>> 00020:    mpirun -np 3  `which relion_refine_mpi` --i
>>>> Runs/001546_ProtRelionClassify2D/input_particles.star --particle_diameter
>>>> 690 --zero_mask  --K 64 --norm  --scale  --o
>>>> Runs/001546_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
>>>> 00021:   RELION version: 3.1.2
>>>> 00022:   Precision: BASE=double, CUDA-ACC=single
>>>> 00023:
>>>> 00024:    === RELION MPI setup ===
>>>> 00025:    + Number of MPI processes             = 3
>>>> 00026:    + Number of threads per MPI process   = 3
>>>> 00027:    + Total number of threads therefore   = 9
>>>> 00028:    + Leader  (0) runs on host            = cryoem01
>>>> 00029:    + Follower     1 runs on host            = cryoem01
>>>> 00030:    + 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 = 448.252 Gb.
>>>> 00044:    Copying particles to scratch directory:
>>>> /data1/new_scratch/relion_volatile/
>>>> 00045:   000/??? sec ~~(,_,">
>>>>                [oo]
>>>> 00046:      1/  60 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/001546_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) [0x7f657f51a555]
>>>> 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/001546_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/001546_ProtRelionClassify2D/input_particles.star --particle_diameter
>>>> 690 --zero_mask  --K 64 --norm  --scale  --o
>>>> Runs/001546_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/001546_ProtRelionClassify2D/input_particles.star --particle_diameter
>>>> 690 --zero_mask  --K 64 --norm  --scale  --o
>>>> Runs/001546_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 12:33:29.230213
>>>> 00085:   *** Last status is failed
>>>> 00086:   ------------------- PROTOCOL FAILED (DONE 2/3)
>>>>
>>>>
>>>> Cryosparc (in SCIPION) requires CTF to run.
>>>>
>>>>
>>>>
>>>> Thais is where I am now.
>>>>
>>>> Perhaps there is a solution?
>>>>
>>>>
>>>> Sincerely,
>>>> Dmitry
>>>>
>>>>
>>>>
>>>> On 18. May 2021, at 14:16, Pablo Conesa <pc...@cn...> wrote:
>>>>
>>>> Dear Dmitry, the import of CS metadata files (*.cs) is not supported in
>>>> Scipion. Does CS has an option to export to star files. It rings a bell.
>>>> On 18/5/21 9:53, Dmitry Semchonok wrote:
>>>>
>>>> Dear Grigory,
>>>>
>>>>
>>>> The files are in mrc format.
>>>>
>>>>
>>>> Please, let me try to explain more plan:
>>>>
>>>>  I have a project in cryosparc. There I have cryosparc selected 2D
>>>> classes. I want to export the particles of those classes into SCIPION.
>>>>
>>>>  So I I pressed Export (fig 1) and the program(cryosparc) created the
>>>> folder with mrc  + other files (fig 2;3). I looked into J48 and found many
>>>> *.mrc files of the particles. But it is not 1 mrc = 1 particle. It seems to
>>>> be a mrc stuck - so I have several files inside 1 *.mrc  (fig 4) (you can
>>>> also notice that they all have different sizes)
>>>>
>>>>  So I need to export them somehow in SCIPION
>>>>
>>>>  For that, I used the SCIPION export - images protocol where for the
>>>> files to add I put *.mrc. But the protocol seems to be added only 1 mrc as
>>>> 1 picture and instead of having 46392 particles I have ~600 particles.
>>>>
>>>>  (Also the geometry seems not preserved).
>>>>
>>>>
>>>> So my question how to export the particles from cryosparc into SCIPION
>>>> correctly?
>>>>
>>>>
>>>>  Thank you!
>>>>
>>>>
>>>>
>>>>  https://disk.yandex.com/d/Fv3Q1lpwEzSisg
>>>>
>>>>  Sincerely,
>>>>
>>>> Dmitry
>>>>
>>>>
>>>>
>>>> On 17. May 2021, at 18:12, Grigory Sharov <sha...@gm...>
>>>> wrote:
>>>>
>>>> Hi Dmitry,
>>>>
>>>> mrc stacks should have "mrcs" extension. Is this the problem you are
>>>> getting?
>>>>
>>>> Best regards,
>>>> Grigory
>>>>
>>>>
>>>> --------------------------------------------------------------------------------
>>>> Grigory Sharov, Ph.D.
>>>>
>>>> MRC Laboratory of Molecular Biology,
>>>> Francis Crick Avenue,
>>>> Cambridge Biomedical Campus,
>>>> Cambridge CB2 0QH, UK.
>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>>>> e-mail: gs...@mr...
>>>>
>>>>
>>>> On Mon, May 17, 2021 at 4:49 PM Dmitry Semchonok <Sem...@gm...>
>>>> wrote:
>>>>
>>>>> Dear colleagues,
>>>>>
>>>>>  I would like to export the particles from cryosparc to SCIPION.
>>>>>
>>>>>  How to do that?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> What I tried:
>>>>>
>>>>>
>>>>> 1.     In cryosparc I pressed Export – to export the particles I am
>>>>> interested in.
>>>>>
>>>>> 2.     In the folder Export – I found many mrc stacks with particles
>>>>> in each.
>>>>>
>>>>> 3.     I tried to export them to SCIPION using Export particles but
>>>>> instead of reading each stack and combine them in the 1 dataset I received
>>>>> 1 particle / per each mrc stack.
>>>>>
>>>>>
>>>>> Any ideas?
>>>>>
>>>>>
>>>>> Thank you
>>>>>
>>>>>  Sincerely,
>>>>>
>>>>> Dmitry
>>>>>
>>>>> _______________________________________________
>>>>> scipion-users mailing list
>>>>> sci...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>
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>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>> --
>>>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team*
>>>> _______________________________________________
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>>>>
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>> _______________________________________________
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>> --
>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team*
>> _______________________________________________
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>> --
>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>>
>
>
> _______________________________________________
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