Re: [scipion-users] relion 3D auto refinement error (after Bayesian polishing)

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

Hi,

this error is described in Relion FAQ

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 Sun, Jul 11, 2021 at 2:56 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear Grigory,
>
>
>
> New error:
>
> ERROR:
>
>
>
> Any suggestions.
>
>
>
> Thank you
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> No orientation was found as better than any other.
>
>
>
> A particle image was compared to the reference and resulted in all-zero
>
> weights (for all orientations). This should not happen, unless your data
>
> has very special characteristics. This has historically happened for some
>
> lower-precision calculations, but multiple fallbacks have since been
>
> implemented. Please report this error to the relion developers at
>
>
>
>                  github.com/3dem/relion/issues
>
>
>
> [dataanalysisserver1:123461] 5 more processes have sent help message
> help-mpi-api.txt / mpi-abort
>
> [dataanalysisserver1:123461] Set MCA parameter "orte_base_help_aggregate"
> to 0 to see all help / error messages
>
> Traceback (most recent call last):
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
>     self._run()
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
>
>     resultFiles = self._runFunc()
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
>
>     return self._func(*self._args)
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 811, in runRelionStep
>
>     self.runJob(self._getProgram(), params)
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1389, in runJob
>
>     self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
>
>     process.runJob(log, programName, params,
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
>     return runCommand(command, env, cwd)
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
>     check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>
>   File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>
>     raise CalledProcessError(retcode, cmd)
>
> subprocess.CalledProcessError: Command ' mpirun -np 7  `which
> relion_refine_mpi` --i Runs/065820_ProtRelionRefine3D/input_particles.star
> --particle_diameter 336 --ctf  --zero_mask  --firstiter_cc  --ini_high 40.0
> --sym c2 --ref_angpix 0.9612 --ref
> Runs/065820_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_map.00.mrc
> --norm  --scale  --o Runs/065820_ProtRelionRefine3D/extra/relion
> --oversampling 1 --flatten_solvent  --pad 2 --skip_gridding
> --auto_local_healpix_order 4 --healpix_order 2 --offset_range 5.0
> --offset_step 2.0 --auto_refine  --split_random_halves
> --low_resol_join_halves 40 --solvent_mask
> Runs/065820_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine_2.mrc
> --dont_combine_weights_via_disc  --scratch_dir
> /home/user/Data/ScipionUserData/scratch --pool 24 --gpu   --j 6' returned
> non-zero exit status 1.
>
> [31mProtocol failed: Command ' mpirun -np 7  `which relion_refine_mpi` --i
> Runs/065820_ProtRelionRefine3D/input_particles.star --particle_diameter 336
> --ctf  --zero_mask  --firstiter_cc  --ini_high 40.0 --sym c2 --ref_angpix
> 0.9612 --ref
> Runs/065820_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_map.00.mrc
> --norm  --scale  --o Runs/065820_ProtRelionRefine3D/extra/relion
> --oversampling 1 --flatten_solvent  --pad 2 --skip_gridding
> --auto_local_healpix_order 4 --healpix_order 2 --offset_range 5.0
> --offset_step 2.0 --auto_refine  --split_random_halves
> --low_resol_join_halves 40 --solvent_mask
> Runs/065820_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine_2.mrc
> --dont_combine_weights_via_disc  --scratch_dir
> /home/user/Data/ScipionUserData/scratch --pool 24 --gpu   --j 6' returned
> non-zero exit status 1.[0m
>
> [35mFAILED[0m: runRelionStep, step 2, time 2021-07-11 15:45:45.010561
>
> *** Last status is failed
>
> [32m------------------- PROTOCOL FAILED (DONE 2/3)[0m
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Grigory Sharov <sha...@gm...>
> *Sent: *Sunday, July 11, 2021 2:48 PM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Subject: *Re: [scipion-users] relion 3D auto refinement error (after
> Bayesian polishing)
>
>
>
> Hi,
>
>
>
> I haven't seen such an error before but I would guess your input mask file
> is corrupted.
>
> 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 Sat, Jul 10, 2021 at 7:58 PM Dmitry A. Semchonok <sem...@gm...>
> wrote:
>
> Thank you Grigory,
>
>
>
> But now the next error -
>
>
>
> RUNNING PROTOCOL -----------------
>
> 00002:   Hostname: localhost4.localdomain4
>
> 00003:   PID: 108841
>
> 00004:   pyworkflow: 3.0.16
>
> 00005:   plugin: relion
>
> 00006:   plugin v: 3.1.2
>
> 00007:   currentDir:
> /home/user/Data/ScipionUserData/projects/Colette__03_06__20
>
> 00008:   workingDir: Runs/065340_ProtRelionRefine3D
>
> 00009:   runMode: Restart
>
> 00010:             MPI: 7
>
> 00011:         threads: 6
>
> 00012:   relion_image_handler:
> /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so.5: no
> version information available (required by relion_image_handler)
>
> 00013:   000/??? sec
> ~~(,_,">                                                          [oo]
>
> 00014:      3/   3 sec
> ..........................................................~~(,_,">
>
> 00015:   ** Running command:  relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine_2.mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine_2.mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0
>
> 00016:    Starting at step: 1
>
> 00017:    Running steps
>
> 00018:   STARTED: convertInputStep, step 1, time 2021-07-10 20:53:24.092629
>
> 00019:   Converting set from 'Runs/065197_ProtUserSubSet/particles.sqlite'
> into 'Runs/065340_ProtRelionRefine3D/input_particles.star'
>
> 00020:   relion_image_handler:
> /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so.5: no
> version information available (required by relion_image_handler)
>
> 00021:   000/??? sec
> ~~(,_,">                                                          [oo]in:
> /home/user/Data/Software/scipion3/software/em/relion-3.1.2/src/multidim_array.h,
> line 678
>
> 00022:   ERROR:
>
> 00023:   coreAllocate:Cannot allocate a negative number of bytes
>
> 00024:   === Backtrace  ===
>
> 00025:   relion_image_handler(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x4bc051]
>
> 00026:
> relion_image_handler(_ZN13MultidimArrayI8tComplexIdEE12coreAllocateEv+0x25e)
> [0x44826e]
>
> 00027:
> relion_image_handler(_ZN13MultidimArrayI8tComplexIdEE9initZerosEllll+0x168)
> [0x4b2818]
>
> 00028:
> relion_image_handler(_Z22windowFourierTransformI8tComplexIdEEvR13MultidimArrayIT_ES5_l+0x75)
> [0x4b2965]
>
> 00029:   relion_image_handler(_Z9resizeMapR13MultidimArrayIdEi+0x378)
> [0x4acfc8]
>
> 00030:
> relion_image_handler(_ZN24image_handler_parameters18perImageOperationsER5ImageIdER8FileNamed+0x969)
> [0x457eb9]
>
> 00031:   relion_image_handler(_ZN24image_handler_parameters3runEv+0x2363)
> [0x45d403]
>
> 00032:   relion_image_handler(main+0x31) [0x4392e1]
>
> 00033:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f1a1750d555]
>
> 00034:   relion_image_handler() [0x43cf9f]
>
> 00035:   ==================
>
> 00036:   ERROR:
>
> 00037:   coreAllocate:Cannot allocate a negative number of bytes
>
> 00038:   convertBinaryFiles: creating soft links.
>
> 00039:      Root: Runs/065340_ProtRelionRefine3D/extra/input ->
> Runs/064819_ProtRelionBayesianPolishing/extra
>
> 00040:   ** Running command:  relion_image_handler --i
> Runs/065419_ProtImportVolumes/extra/import_cryosparc_P12_J26_008_volume_map.mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/import_cryosparc_P12_J26_008_volume_map.00.mrc
> --angpix 9612.00000 --rescale_angpix 0.96120 --new_box 384
>
> 00041:   Traceback (most recent call last):
>
> 00042:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
> 00043:       self._run()
>
> 00044:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
>
> 00045:       resultFiles = self._runFunc()
>
> 00046:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
>
> 00047:       return self._func(*self._args)
>
> 00048:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 803, in convertInputStep
>
> 00049:       self._convertRef()
>
> 00050:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 1249, in _convertRef
>
> 00051:       self._convertVol(refVols[0])
>
> 00052:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 1232, in _convertVol
>
> 00053:       relion.convert.convertMask(inputVol, outputFn, newPix=newPix,
>
> 00054:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py",
> line 224, in convertMask
>
> 00055:       pwutils.runJob(None, 'relion_image_handler', params,
> env=Plugin.getEnviron())
>
> 00056:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
> 00057:       return runCommand(command, env, cwd)
>
> 00058:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
> 00059:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
>
> 00060:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>
> 00061:       raise CalledProcessError(retcode, cmd)
>
> 00062:   subprocess.CalledProcessError: Command ' relion_image_handler --i
> Runs/065419_ProtImportVolumes/extra/import_cryosparc_P12_J26_008_volume_map.mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/import_cryosparc_P12_J26_008_volume_map.00.mrc
> --angpix 9612.00000 --rescale_angpix 0.96120 --new_box 384' returned
> non-zero exit status 1.
>
> 00063:   Protocol failed: Command ' relion_image_handler --i
> Runs/065419_ProtImportVolumes/extra/import_cryosparc_P12_J26_008_volume_map.mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/import_cryosparc_P12_J26_008_volume_map.00.mrc
> --angpix 9612.00000 --rescale_angpix 0.96120 --new_box 384' returned
> non-zero exit status 1.
>
> 00064:   FAILED: convertInputStep, step 1, time 2021-07-10 20:53:37.235999
>
> 00065:   *** Last status is failed
>
> 00066:   ------------------- PROTOCOL FAILED (DONE 1/3)
>
>
>
>
>
> *From: *Grigory Sharov <sha...@gm...>
> *Sent: *Saturday, July 10, 2021 5:14 PM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Subject: *Re: [scipion-users] relion 3D auto refinement error (after
> Bayesian polishing)
>
>
>
> Hi Dmitry,
>
>
>
> This one is easy. You need to remove brackets from the file name Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> before import
>
>
>
> On Sat, Jul 10, 2021, 15:47 Dmitry A. Semchonok <sem...@gm...>
> wrote:
>
> Dear Grigory & colleagues,
>
>
>
> During relion 3D refinement I received the error – please see below.
>
>
>
> Prehistory – I run the Bayesian polishing with the relion 3D refinement
> dataset (syntax error near unexpected token `(').
>
> I suspect there are some errors in Bayesian polishing outcome dataset.
> Some of them I fixed by deleting black images.
>
>
>
> So the question is how to fix the remaining errors to let the relion 3D
> refinement run?
>
>
>
> Thank you in advance,
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> RUNNING PROTOCOL -----------------
>
> 00002:   Hostname: localhost4.localdomain4
>
> 00003:   PID: 86173
>
> 00004:   pyworkflow: 3.0.16
>
> 00005:   plugin: relion
>
> 00006:   plugin v: 3.1.2
>
> 00007:   currentDir:
> /home/user/Data/ScipionUserData/projects/Colette__03_06__20
>
> 00008:   workingDir: Runs/065340_ProtRelionRefine3D
>
> 00009:   runMode: Continue
>
> 00010:             MPI: 7
>
> 00011:         threads: 6
>
> 00012:   /bin/sh: -c: line 0: syntax error near unexpected token `('
>
> 00013:   /bin/sh: -c: line 0: ` relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0'
>
> 00014:   ** Running command:  relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0
>
> 00015:   Traceback (most recent call last):
>
> 00016:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
> 00017:       self._run()
>
> 00018:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1361, in _run
>
> 00019:       self._insertAllSteps()  # Define steps for execute later
>
> 00020:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 740, in _insertAllSteps
>
> 00021:       self._insertRelionStep()
>
> 00022:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 751, in _insertRelionStep
>
> 00023:       self._setNormalArgs(args)
>
> 00024:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 969, in _setNormalArgs
>
> 00025:       self._setBasicArgs(args)
>
> 00026:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 1038, in _setBasicArgs
>
> 00027:       self._setMaskArgs(args)
>
> 00028:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 1065, in _setMaskArgs
>
> 00029:       mask = relion.convert.convertMask(self.referenceMask.get(),
>
> 00030:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py",
> line 224, in convertMask
>
> 00031:       pwutils.runJob(None, 'relion_image_handler', params,
> env=Plugin.getEnviron())
>
> 00032:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
> 00033:       return runCommand(command, env, cwd)
>
> 00034:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
> 00035:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
>
> 00036:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>
> 00037:       raise CalledProcessError(retcode, cmd)
>
> 00038:   subprocess.CalledProcessError: Command ' relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0' returned non-zero exit status 1.
>
> 00039:   ------------------- PROTOCOL FAILED (DONE 0/0)
>
>
>
>
>
> _______________________________________________
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>
>
>
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>
>
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>