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From: Dmitry A. S. <sem...@gm...> - 2020-07-07 19:54:48
|
Dear colleagues, I would like to ask how to subtract the micelles density around your membrane protein in the proper way? What are the steps? Thank you! Sincerely, Dmitry |
|
From: Pablo C. <pc...@cn...> - 2020-06-23 07:28:41
|
Hi, this is not actually an error. It's just a message saying that your BUILD section differs from the relased template. Actually it is what has to happen when you configure CONDA inside scipion. It should be fine to continue. On 23/6/20 0:40, Dmitry A. Semchonok wrote: > Dear colleagues, > > after running the scipion config I got the following error > > > What is the way for fixing that? > > Thank you! > > Sincerely, > Dmitry > > > > [root@data scipion]# scipion config > > Scipion v2.0 (2019-04-23) Diocletian > > >>>>> python /usr/local/scipion/pyworkflow/apps/pw_config.py > Found differences between the configuration file > /usr/local/scipion/config/scipion.conf > and the template file > /usr/local/scipion/pyworkflow/templates/scipion.template > *In section BUILD, option CONDA_ACTIVATION_CMD exists in the > configuration file but not in the template.* > All the expected sections and options found in > /usr/local/scipion/config/protocols.conf > All the expected sections and options found in > /usr/local/scipion/config/hosts.conf > All the expected sections and options found in > /root/.config/scipion/scipion.conf > Checking paths in /usr/local/scipion/config/scipion.conf ... > All seems fine with /usr/local/scipion/config/scipion.conf > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2020-06-23 07:26:21
|
Dear Dmitry.....how are ctf inputs....is the estimation correct or have some failed. Explore the values visually. On 23/6/20 0:29, Dmitry A. Semchonok wrote: > Dear colleagues, > > I would like to run xmipp3-ctf concensus but I got the following error. > > Could you please help? > > thank you! > > Sincerely, > Dmitry > > File 'Runs/010692_XmippProtCTFConsensus/logs/run.stdout' doesn't > existFile 'Runs/010692_XmippProtCTFConsensus/logs/run.stdout' doesn't > exist00001: RUNNING PROTOCOL ----------------- > 00002: HostName: dataanalysisserver1 > 00003: PID: 38890 > 00004: Scipion: v2.0 (2019-04-23) Diocletian > 00005: currentDir: > /home/user/Data/ScipionUserData/projects/Colette__03_06__20 > 00006: workingDir: Runs/010692_XmippProtCTFConsensus > 00007: runMode: Restart > 00008: MPI: 1 > 00009: threads: 1 > 00010: Starting at step: 1 > 00011: Running steps > 00012: STARTED: _computeCTFDiscrepancy, step 1 > 00013: 2020-06-23 00:25:58.360157 > 00014: float() argument must be a string or a number > 00015: Problems found converting metadata: > 00016: Label id = 132 > 00017: Attribute = _fitQuality > 00018: Value = None > 00019: Value type = <type 'float'> > 00020: Traceback (most recent call last): > 00021: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", > line 186, in run > 00022: self._run() > 00023: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", > line 237, in _run > 00024: resultFiles = self._runFunc() > 00025: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", > line 233, in _runFunc > 00026: return self._func(*self._args) > 00027: File > "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/protocols/protocol_ctf_consensus.py", > line 504, in _computeCTFDiscrepancy > 00028: self._ctfToMd(ctf1, md1) > 00029: File > "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/protocols/protocol_ctf_consensus.py", > line 482, in _ctfToMd > 00030: xmipp3.convert.ctfModelToRow(ctf, ctfRow) > 00031: File > "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/convert/convert.py", > line 635, in ctfModelToRow > 00032: extraLabels=CTF_EXTRA_LABELS) > 00033: File > "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/convert/convert.py", > line 252, in objectToRow > 00034: raise e > 00035: TypeError: float() argument must be a string or a number > 00036: Protocol failed: float() argument must be a string or a number > 00037: FAILED: _computeCTFDiscrepancy, step 1 > 00038: 2020-06-23 00:26:16.638520 > 00039: *** Last status is failed > 00040: ------------------- PROTOCOL FAILED (DONE 1/1815) > NameError: name 'sys' is not defined > > ======================================== > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Dmitry A. S. <sem...@gm...> - 2020-06-22 22:40:43
|
Dear colleagues, after running the scipion config I got the following error What is the way for fixing that? Thank you! Sincerely, Dmitry [root@data scipion]# scipion config Scipion v2.0 (2019-04-23) Diocletian >>>>> python /usr/local/scipion/pyworkflow/apps/pw_config.py Found differences between the configuration file /usr/local/scipion/config/scipion.conf and the template file /usr/local/scipion/pyworkflow/templates/scipion.template In section BUILD, option CONDA_ACTIVATION_CMD exists in the configuration file but not in the template. All the expected sections and options found in /usr/local/scipion/config/protocols.conf All the expected sections and options found in /usr/local/scipion/config/hosts.conf All the expected sections and options found in /root/.config/scipion/scipion.conf Checking paths in /usr/local/scipion/config/scipion.conf ... All seems fine with /usr/local/scipion/config/scipion.conf |
|
From: Dmitry A. S. <sem...@gm...> - 2020-06-22 22:29:51
|
Dear colleagues, I would like to run xmipp3-ctf concensus but I got the following error. Could you please help? thank you! Sincerely, Dmitry File 'Runs/010692_XmippProtCTFConsensus/logs/run.stdout' doesn't existFile 'Runs/010692_XmippProtCTFConsensus/logs/run.stdout' doesn't exist00001: RUNNING PROTOCOL ----------------- 00002: HostName: dataanalysisserver1 00003: PID: 38890 00004: Scipion: v2.0 (2019-04-23) Diocletian 00005: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20 00006: workingDir: Runs/010692_XmippProtCTFConsensus 00007: runMode: Restart 00008: MPI: 1 00009: threads: 1 00010: Starting at step: 1 00011: Running steps 00012: STARTED: _computeCTFDiscrepancy, step 1 00013: 2020-06-23 00:25:58.360157 00014: float() argument must be a string or a number 00015: Problems found converting metadata: 00016: Label id = 132 00017: Attribute = _fitQuality 00018: Value = None 00019: Value type = <type 'float'> 00020: Traceback (most recent call last): 00021: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in run 00022: self._run() 00023: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in _run 00024: resultFiles = self._runFunc() 00025: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc 00026: return self._func(*self._args) 00027: File "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/protocols/protocol_ctf_consensus.py", line 504, in _computeCTFDiscrepancy 00028: self._ctfToMd(ctf1, md1) 00029: File "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/protocols/protocol_ctf_consensus.py", line 482, in _ctfToMd 00030: xmipp3.convert.ctfModelToRow(ctf, ctfRow) 00031: File "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/convert/convert.py", line 635, in ctfModelToRow 00032: extraLabels=CTF_EXTRA_LABELS) 00033: File "/usr/local/scipion/software/lib/python2.7/site-packages/xmipp3/convert/convert.py", line 252, in objectToRow 00034: raise e 00035: TypeError: float() argument must be a string or a number 00036: Protocol failed: float() argument must be a string or a number 00037: FAILED: _computeCTFDiscrepancy, step 1 00038: 2020-06-23 00:26:16.638520 00039: *** Last status is failed 00040: ------------------- PROTOCOL FAILED (DONE 1/1815) NameError: name 'sys' is not defined ======================================== |
|
From: Grigory S. <sha...@gm...> - 2020-06-16 10:48:39
|
Dear Maria,
the gautomatch binary you are using is for cuda 8. Recently, new gctf /
gautomatch binaries have become available for cuda 10. If you re-install
the binaries (scipion uninstallb gautomatch, then scipion
installb gautomatch) you will see
Gautomatch_v0.56_sm30-75_cu10.1 file in the bin folder that you might try.
Don't forget to change GAUTOMATCH var in scipion.conf to point to the new
binary.
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, Jun 16, 2020 at 11:26 AM Maria Del Mar Perez Ruiz <
mar...@cp...> wrote:
> Dear Scipion team,
>
>
>
> I am trying to run Gautomatch v0.56 in Scipion (v2.0 Diocletian) and I
> have this issue (see below).
>
>
>
> My question is what’s it going on? And if is it related with our CUDA
> version? We have CUDA version 10.0.130 and GPU Cuda version 10.2.
>
> If I add GAUTOMATCH_CUDA_LIB variable to the config file with the path
> where CUDA10 is, I have the same issue.
>
> Is there any CUDA10 version for Scipion?
>
>
>
> Thank you so much for your help!
>
>
>
>
>
> 02662: STARTED: pickMicrographStep, step 28
> 02663: 2020-06-16 10:08:18.670414
> 02664: Picking micrograph:
> Runs/000388_ProtRelionMotioncor/extra/FoilHole_18276562_Data_18277147_18277148_20190719_1447_Fractions_aligned_mic_DW.mrc
>
> 02665:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> Runs/002849_ProtGautomatch/tmp/mic_000029/*.mrc -T
> Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5
> --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30
> --detect_ice 1 --T_norm_type 1 --do_bandpass 1
> 02666:
> ***************************************************************************************************
> 02667: Version:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> v0.56, updated on 2017-07-30
> 02668: Author: Kai Zhang@MRC Laboratory of Molecular Biology
> 02669: Contact: kz...@mr...
> 02670: Description: This is a GPU accelerated program for fully
> automatic particle picking.
> 02671: Note: Still under development, to be released soon ...
> 02672:
> ***************************************************************************************************
> 02673: Usage:
> 02674:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> [options] <micrographs>
> 02675:
> 02676: Options:
> 02677: Basic options: default values, description:
> 02678: --apixM 1.34 Pixel size of the
> micrograph, in angstrom
> 02679: --diameter 400 Particle diameter, in
> angstrom;
> 02680: --T NONE Particle picking templates
> in 2D MRC stack; must provide the correct pixel size if not the same as
> micrograph; auto-generated if not provided;
> 02681: --apixT 1.34 Pixel size of the templates,
> in angstrom; will be the same as --apixM if not set.
> 02682:
> 02683: Additional options(not suggested, only try to optimize in
> difficult cases), default values and description:
> 02684: --ang_step 5 Angular step size for
> picking, invalid for auto-templates
> 02685: --speed 2 Speed level {0,1,2,3,4}, the
> bigger the faster, but less accurate.
> 02686: --boxsize 128 Box size, in pixel, NOT in
> angstrom; a suggested value will be automatically calculated by --diameter
> and --apixM
> 02687: --min_dist 300 Minimum distance between
> particles in angstrom; 0.9~1.1X diameter; can be 0.3~0.5 for filament-like
> particle
> 02688: --cc_cutoff 0.1 Cross-correlation cutoff,
> 0.2~0.4 normally; Try to select several typical micrographs to optimize
> this value.
> 02689: Alternatively, it will be
> even faster if you use a small value, e.g. 0.1, first and then use '
> box_filter.com' or 'box_filter2rl.com' to filter the box files afterwards.
> 02690: --lsigma_D 200 Diameter for estimation of
> local sigma, in angstrom
> 02691: --lsigma_cutoff 1.3 Local sigma cutoff (relative
> value), 1.2~1.5 should be a good range; normally a value >1.2 will be ice,
> protein aggregation or contamination
> 02692: --lave_D 400 Diameter for estimation of
> local average, in angstrom, 0.5~2.0X particle diameter suggested;
> 02693: However, if you have
> 'sharp'/'small' ice or any 'dark'/'bright' dots, use a smaller value will
> be much better to get rid of these areas.
> 02694: --lave_max 2.0 Local average cutoff
> (relative value), any pixel value above that will be considered as
> ice/aggregation/carbon etc.
> 02695: --lave_min -1.0 Local average cutoff
> (relative value), any pixel value below that will be considered as
> ice/aggregation/carbon etc.
> 02696: For 'black' cryoEM
> micrograph, set this to very small value e.g. -10.0 will not reject any
> 'black' dots in general.
> 02697: --lp 30 Low-pass filter to increase
> the contrast of raw micrographs, suggested range 20~50Å. This low-pass is
> after ice/aggregation detection.
> 02698: --hp 1000 High-pass filter to get rid
> of the global background of raw micrographs, suggested range 200~2000Å.
> This high-pass is after ice/aggregation detection.
> 02699: --do_pre_filter Specify to get rid of
> severely gradient background before ice/aggregation/carbon detection. This
> is not normally suggested because it might affect ice/carbon detection.
> 02700: --pre_lp 8.0 The same as --lp, but before
> the ice/contamination detection, might be better in severely gradient ice.
> 02701: Does not matter to use both
> --lp and --pre_lp, but suggested to use much smaller --pre_lp for better
> ice/contamination detection.
> 02702: --pre_hp 1000 The same as --hp, but before
> the ice/contamination detection, might be better in severely gradient ice.
> 02703: Otherwise, do not use
> --pre_hp or use a very big value.
> 02704: --detect_ice 1 Specify 0 to avoid
> ice/aggregation/carbon detection.
> 02705: --T_norm_type 1 Specify the type of Template
> normalization, 1, 2 or 3 allowed.
> 02706: --do_bandpass 1 Specify 0 to skip the
> bandpass; By default it will do bandpass filter.
> 02707: CTF options(not effective in this verion):
> 02708: --do_ctf Specify this option to do
> CTF determination and correction for better picking
> 02709: --do_local_ctf Specify this option to do
> local CTF determination and correction for each picked particle
> 02710: --kV 300 High tension in Kilovolt,
> typically 300, 200 or 120
> 02711: --cs 2.7 Spherical aberration, in
> millimeter
> 02712: --ac 0.1 Amplitude contrast; normal
> range 0.04~0.1; pure ice 0.04, carbon 0.1; but doesn't matter too much if
> using wrong value
> 02713:
> 02714: I/O options:
> 02715: --write_ccmax_mic Specify to write out
> cross-correlation files, in MRC stack
> 02716: --write_pf_mic Specify to write out
> phase-flipped(pf) micrographs(mic)
> 02717: --write_pref_mic Specify to write out
> pre-filted(pref) micrographs(mic)
> 02718: --write_bg_mic Specify to write out
> estimated background(bg) of the micrographs(mic)
> 02719: --write_bgfree_mic Specify to write out
> background subtracted (bgfree) micrographs(mic)
> 02720: --write_lsigma_mic Specify to write out local
> sigma (lsigma) micrographs(mic)
> 02721: --write_mic_mask Specify to write out the
> auto-detected mask (ice, contamination, aggregation, carbon edge etc.) by
> --lsigma_cutoff or --lave_max or --lave_max
> 02722: --exclusive_picking Specify to pick the
> particles by pre-defined coordinates that will be excluded.
> 02723: This is useful, when you
> have done 2D classification and provide the rubbish particles that
> Gautomatch will automatically exclude
> 02724: --excluded_suffix The suffix of coordinates to
> be excluded. Relion .star and EMAN .box file are both accepted, extended
> .box file format in Gautomach preferred.
> 02725: For example, if
> --excluded_suffix _rubbish.box is provided for mic0002.mrc, then Gautomatch
> will try to find mic0002_rubbish.box and exclude them during picking.
> 02726: --mask_excluded Specify this option to mask
> out the excluded coordinates so that it will nerve be taken into account in
> any step of processing, even not in the normalization step.
> 02727: This is helpful if the
> artifacts are extremely different from normal area of the micrographs.
> 02728: --global_excluded_box NONE Provide a coordinate
> .box/.star file to exclude these special coordinates completely from all
> micrographs before any processing.
> 02729: So generally, these area
> will not involve in normalization, ice/aggregation/carbon detection. They
> are completely gone.
> 02730: Note, the --excluded_suffix
> option is used for individual files.
> 02731: --do_unfinished Specify to autopick the
> unfinished micrographs
> 02732: --dont_invertT Whether to invert template
> contrast. VERY IMPORTANT!!! By default, the program will invert the 'white'
> templates to 'black' before picking.
> 02733: specify this option to avoid
> contrast inversion if the micrographs and templates have the same contrast
> 02734: --extract_raw Specify to extract particle
> from raw micrograph
> 02735: --extract_pf Specify to extract particle
> from phase-flipped micrograph; will write a new stack and will not
> overwrite raw particle stack
> 02736: --gid 0 GPU id, normally it's 0, use
> gpu_info to get information of all available GPUs.
> 02737:
> 02738: Example:
> 02739:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.58 --diameter 300 Micrographs/Falcon*.mrc (auto-generated
> templates for 'black' cryoEM micrograph)
> 02740:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 2.16
> Micrographs/Falcon*.mrc (for 'white' templates and 'black' micrograph
> 02741:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 3.2
> --dont_invertT Micrographs/Falcon*.mrc (for 'black' templates and 'black'
> micrograph)
> 02742:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 --boxsize 360 --write_bgfree_mic
> --write_lsigma_mic --extract_raw --write_ccmax Micrographs/Falcon*.mrc
> (suggested for manual diagnosis using the different types of output
> micrographs)
> 02743:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> test?.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T
> templates_lp40_3.2A.mrcs --write_pref_mic --lsigma_cutoff 1.2 --cc_cutoff
> 0.18 --lave_D 80 --lave_min -0.8 --lave_max 1.2 --exclusive_picking
> --excluded_suffix _rubbish.star --mask_excluded --write_ccmax_mic
> --write_pf_mic --write_pref_mic --write_bg_mic --write_bgfree_mic
> --write_lsigma_mic --write_mic_mask --extract_raw --do_pre_filter 1
> --pre_lp 10 --pre_hp 1000 --lp 40 --boxsize 432
> 02744: --help Print full help document
> 02745: Error in function gautomatch_help_exit(), file automatch56.cu on
> line 1322: Failed to find any usable GPU device!! Exit now!
> 02746: Traceback (most recent call last):
> 02747: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 151,
> in run
> 02748: self.step._run() # not self.step.run() , to avoid race
> conditions
> 02749: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 237,
> in _run
> 02750: resultFiles = self._runFunc()
> 02751: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 233,
> in _runFunc
> 02752: return self._func(*self._args)
> 02753: File
> "/services/tools/scipion/2.0.0/pyworkflow/em/protocol/protocol_particles_picking.py",
> line 242, in pickMicrographStep
> 02754: self._pickMicrograph(mic, *args)
> 02755: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py",
> line 327, in _pickMicrograph
> 02756: self._pickMicrographList([mic], args)
> 02757: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py",
> line 355, in _pickMicrographList
> 02758: runJob=self.runJob)
> 02759: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/__init__.py",
> line 104, in runGautomatch
> 02760: runJob(cls.getProgram(), args, env=environ)
> 02761: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 1311,
> in runJob
> 02762: self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 02763: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 70,
> in runJob
> 02764: env=env, cwd=cwd, gpuList=self.getGpuList())
> 02765: File
> "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 52, in
> runJob
> 02766: return runCommand(command, env, cwd)
> 02767: File
> "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 67, in
> runCommand
> 02768: env=env, cwd=cwd)
> 02769: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/subprocess.py", line
> 190, in check_call
> 02770: raise CalledProcessError(retcode, cmd)
> 02771: CalledProcessError: Command
> '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> Runs/002849_ProtGautomatch/tmp/mic_000027/*.mrc -T
> Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5
> --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30
> --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit
> status 1
> 02772: Picking micrograph:
> Runs/000388_ProtRelionMotioncor/extra/FoilHole_18276563_Data_18277114_18277115_20190719_1448_Fractions_aligned_mic_DW.mrc
>
> 02773: Protocol failed: Command
> '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> Runs/002849_ProtGautomatch/tmp/mic_000027/*.mrc -T
> Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5
> --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30
> --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit
> status 1
> 02774:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> Runs/002849_ProtGautomatch/tmp/mic_000031/*.mrc -T
> Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5
> --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30
> --detect_ice 1 --T_norm_type 1 --do_bandpass 1
> 02775:
> ***************************************************************************************************
> 02776: Version:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> v0.56, updated on 2017-07-30
> 02777: Author: Kai Zhang@MRC Laboratory of Molecular Biology
> 02778: Contact: kz...@mr...
> 02779: Description: This is a GPU accelerated program for fully
> automatic particle picking.
> 02780: Note: Still under development, to be released soon ...
> 02781:
> ***************************************************************************************************
> 02782: Usage:
> 02783:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> [options] <micrographs>
> 02784:
> 02785: Options:
> 02786: Basic options: default values, description:
> 02787: --apixM 1.34 Pixel size of the
> micrograph, in angstrom
> 02788: --diameter 400 Particle diameter, in
> angstrom;
> 02789: --T NONE Particle picking templates
> in 2D MRC stack; must provide the correct pixel size if not the same as
> micrograph; auto-generated if not provided;
> 02790: --apixT 1.34 Pixel size of the templates,
> in angstrom; will be the same as --apixM if not set.
> 02791:
> 02792: Additional options(not suggested, only try to optimize in
> difficult cases), default values and description:
> 02793: --ang_step 5 Angular step size for
> picking, invalid for auto-templates
> 02794: --speed 2 Speed level {0,1,2,3,4}, the
> bigger the faster, but less accurate.
> 02795: --boxsize 128 Box size, in pixel, NOT in
> angstrom; a suggested value will be automatically calculated by --diameter
> and --apixM
> 02796: --min_dist 300 Minimum distance between
> particles in angstrom; 0.9~1.1X diameter; can be 0.3~0.5 for filament-like
> particle
> 02797: --cc_cutoff 0.1 Cross-correlation cutoff,
> 0.2~0.4 normally; Try to select several typical micrographs to optimize
> this value.
> 02798: Alternatively, it will be
> even faster if you use a small value, e.g. 0.1, first and then use '
> box_filter.com' or 'box_filter2rl.com' to filter the box files afterwards.
> 02799: --lsigma_D 200 Diameter for estimation of
> local sigma, in angstrom
> 02800: --lsigma_cutoff 1.3 Local sigma cutoff (relative
> value), 1.2~1.5 should be a good range; normally a value >1.2 will be ice,
> protein aggregation or contamination
> 02801: --lave_D 400 Diameter for estimation of
> local average, in angstrom, 0.5~2.0X particle diameter suggested;
> 02802: However, if you have
> 'sharp'/'small' ice or any 'dark'/'bright' dots, use a smaller value will
> be much better to get rid of these areas.
> 02803: --lave_max 2.0 Local average cutoff
> (relative value), any pixel value above that will be considered as
> ice/aggregation/carbon etc.
> 02804: --lave_min -1.0 Local average cutoff
> (relative value), any pixel value below that will be considered as
> ice/aggregation/carbon etc.
> 02805: For 'black' cryoEM
> micrograph, set this to very small value e.g. -10.0 will not reject any
> 'black' dots in general.
> 02806: --lp 30 Low-pass filter to increase
> the contrast of raw micrographs, suggested range 20~50Å. This low-pass is
> after ice/aggregation detection.
> 02807: --hp 1000 High-pass filter to get rid
> of the global background of raw micrographs, suggested range 200~2000Å.
> This high-pass is after ice/aggregation detection.
> 02808: --do_pre_filter Specify to get rid of
> severely gradient background before ice/aggregation/carbon detection. This
> is not normally suggested because it might affect ice/carbon detection.
> 02809: --pre_lp 8.0 The same as --lp, but before
> the ice/contamination detection, might be better in severely gradient ice.
> 02810: Does not matter to use both
> --lp and --pre_lp, but suggested to use much smaller --pre_lp for better
> ice/contamination detection.
> 02811: --pre_hp 1000 The same as --hp, but before
> the ice/contamination detection, might be better in severely gradient ice.
> 02812: Otherwise, do not use
> --pre_hp or use a very big value.
> 02813: --detect_ice 1 Specify 0 to avoid
> ice/aggregation/carbon detection.
> 02814: --T_norm_type 1 Specify the type of Template
> normalization, 1, 2 or 3 allowed.
> 02815: --do_bandpass 1 Specify 0 to skip the
> bandpass; By default it will do bandpass filter.
> 02816: CTF options(not effective in this verion):
> 02817: --do_ctf Specify this option to do
> CTF determination and correction for better picking
> 02818: --do_local_ctf Specify this option to do
> local CTF determination and correction for each picked particle
> 02819: --kV 300 High tension in Kilovolt,
> typically 300, 200 or 120
> 02820: --cs 2.7 Spherical aberration, in
> millimeter
> 02821: --ac 0.1 Amplitude contrast; normal
> range 0.04~0.1; pure ice 0.04, carbon 0.1; but doesn't matter too much if
> using wrong value
> 02822:
> 02823: I/O options:
> 02824: --write_ccmax_mic Specify to write out
> cross-correlation files, in MRC stack
> 02825: --write_pf_mic Specify to write out
> phase-flipped(pf) micrographs(mic)
> 02826: --write_pref_mic Specify to write out
> pre-filted(pref) micrographs(mic)
> 02827: --write_bg_mic Specify to write out
> estimated background(bg) of the micrographs(mic)
> 02828: --write_bgfree_mic Specify to write out
> background subtracted (bgfree) micrographs(mic)
> 02829: --write_lsigma_mic Specify to write out local
> sigma (lsigma) micrographs(mic)
> 02830: --write_mic_mask Specify to write out the
> auto-detected mask (ice, contamination, aggregation, carbon edge etc.) by
> --lsigma_cutoff or --lave_max or --lave_max
> 02831: --exclusive_picking Specify to pick the
> particles by pre-defined coordinates that will be excluded.
> 02832: This is useful, when you
> have done 2D classification and provide the rubbish particles that
> Gautomatch will automatically exclude
> 02833: --excluded_suffix The suffix of coordinates to
> be excluded. Relion .star and EMAN .box file are both accepted, extended
> .box file format in Gautomach preferred.
> 02834: For example, if
> --excluded_suffix _rubbish.box is provided for mic0002.mrc, then Gautomatch
> will try to find mic0002_rubbish.box and exclude them during picking.
> 02835: --mask_excluded Specify this option to mask
> out the excluded coordinates so that it will nerve be taken into account in
> any step of processing, even not in the normalization step.
> 02836: This is helpful if the
> artifacts are extremely different from normal area of the micrographs.
> 02837: --global_excluded_box NONE Provide a coordinate
> .box/.star file to exclude these special coordinates completely from all
> micrographs before any processing.
> 02838: So generally, these area
> will not involve in normalization, ice/aggregation/carbon detection. They
> are completely gone.
> 02839: Note, the --excluded_suffix
> option is used for individual files.
> 02840: --do_unfinished Specify to autopick the
> unfinished micrographs
> 02841: --dont_invertT Whether to invert template
> contrast. VERY IMPORTANT!!! By default, the program will invert the 'white'
> templates to 'black' before picking.
> 02842: specify this option to avoid
> contrast inversion if the micrographs and templates have the same contrast
> 02843: --extract_raw Specify to extract particle
> from raw micrograph
> 02844: --extract_pf Specify to extract particle
> from phase-flipped micrograph; will write a new stack and will not
> overwrite raw particle stack
> 02845: --gid 0 GPU id, normally it's 0, use
> gpu_info to get information of all available GPUs.
> 02846:
> 02847: Example:
> 02848:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.58 --diameter 300 Micrographs/Falcon*.mrc (auto-generated
> templates for 'black' cryoEM micrograph)
> 02849:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 2.16
> Micrographs/Falcon*.mrc (for 'white' templates and 'black' micrograph
> 02850:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 3.2
> --dont_invertT Micrographs/Falcon*.mrc (for 'black' templates and 'black'
> micrograph)
> 02851:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 --boxsize 360 --write_bgfree_mic
> --write_lsigma_mic --extract_raw --write_ccmax Micrographs/Falcon*.mrc
> (suggested for manual diagnosis using the different types of output
> micrographs)
> 02852:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> test?.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T
> templates_lp40_3.2A.mrcs --write_pref_mic --lsigma_cutoff 1.2 --cc_cutoff
> 0.18 --lave_D 80 --lave_min -0.8 --lave_max 1.2 --exclusive_picking
> --excluded_suffix _rubbish.star --mask_excluded --write_ccmax_mic
> --write_pf_mic --write_pref_mic --write_bg_mic --write_bgfree_mic
> --write_lsigma_mic --write_mic_mask --extract_raw --do_pre_filter 1
> --pre_lp 10 --pre_hp 1000 --lp 40 --boxsize 432
> 02853: --help Print full help document
> 02854: Error in function gautomatch_help_exit(), file automatch56.cu on
> line 1322: Failed to find any usable GPU device!! Exit now!
> 02855: Traceback (most recent call last):
> 02856: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 151,
> in run
> 02857: self.step._run() # not self.step.run() , to avoid race
> conditions
> 02858: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 237,
> in _run
> 02859: resultFiles = self._runFunc()
> 02860: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 233,
> in _runFunc
> 02861: return self._func(*self._args)
> 02862: File
> "/services/tools/scipion/2.0.0/pyworkflow/em/protocol/protocol_particles_picking.py",
> line 242, in pickMicrographStep
> 02863: self._pickMicrograph(mic, *args)
> 02864: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py",
> line 327, in _pickMicrograph
> 02865: self._pickMicrographList([mic], args)
> 02866: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py",
> line 355, in _pickMicrographList
> 02867: runJob=self.runJob)
> 02868: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/__init__.py",
> line 104, in runGautomatch
> 02869: runJob(cls.getProgram(), args, env=environ)
> 02870: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 1311,
> in runJob
> 02871: self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 02872: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 70,
> in runJob
> 02873: env=env, cwd=cwd, gpuList=self.getGpuList())
> 02874: File
> "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 52, in
> runJob
> 02875: return runCommand(command, env, cwd)
> 02876: File
> "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 67, in
> runCommand
> 02877: env=env, cwd=cwd)
> 02878: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/subprocess.py", line
> 190, in check_call
> 02879: raise CalledProcessError(retcode, cmd)
> 02880: CalledProcessError: Command
> '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> Runs/002849_ProtGautomatch/tmp/mic_000029/*.mrc -T
> Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5
> --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30
> --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit
> status 1
> 02881: FAILED: pickMicrographStep, step 26
> 02882: 2020-06-16 10:08:18.699681
> 02883:
> ***************************************************************************************************
> 02884: Version:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> v0.56, updated on 2017-07-30
> 02885: Author: Kai Zhang@MRC Laboratory of Molecular Biology
> 02886: Contact: kz...@mr...
> 02887: Description: This is a GPU accelerated program for fully
> automatic particle picking.
> 02888: Note: Still under development, to be released soon ...
> 02889:
> ***************************************************************************************************
> 02890: Usage:
> 02891:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> [options] <micrographs>
> 02892:
> 02893: Options:
> 02894: Basic options: default values, description:
> 02895: --apixM 1.34 Pixel size of the
> micrograph, in angstrom
> 02896: --diameter 400 Particle diameter, in
> angstrom;
> 02897: --T NONE Particle picking templates
> in 2D MRC stack; must provide the correct pixel size if not the same as
> micrograph; auto-generated if not provided;
> 02898: --apixT 1.34 Pixel size of the templates,
> in angstrom; will be the same as --apixM if not set.
> 02899:
> 02900: Additional options(not suggested, only try to optimize in
> difficult cases), default values and description:
> 02901: --ang_step 5 Angular step size for
> picking, invalid for auto-templates
> 02902: --speed 2 Speed level {0,1,2,3,4}, the
> bigger the faster, but less accurate.
> 02903: --boxsize 128 Box size, in pixel, NOT in
> angstrom; a suggested value will be automatically calculated by --diameter
> and --apixM
> 02904: --min_dist 300 Minimum distance between
> particles in angstrom; 0.9~1.1X diameter; can be 0.3~0.5 for filament-like
> particle
> 02905: --cc_cutoff 0.1 Cross-correlation cutoff,
> 0.2~0.4 normally; Try to select several typical micrographs to optimize
> this value.
> 02906: Alternatively, it will be
> even faster if you use a small value, e.g. 0.1, first and then use '
> box_filter.com' or 'box_filter2rl.com' to filter the box files afterwards.
> 02907: --lsigma_D 200 Diameter for estimation of
> local sigma, in angstrom
> 02908: --lsigma_cutoff 1.3 Local sigma cutoff (relative
> value), 1.2~1.5 should be a good range; normally a value >1.2 will be ice,
> protein aggregation or contamination
> 02909: --lave_D 400 Diameter for estimation of
> local average, in angstrom, 0.5~2.0X particle diameter suggested;
> 02910: However, if you have
> 'sharp'/'small' ice or any 'dark'/'bright' dots, use a smaller value will
> be much better to get rid of these areas.
> 02911: --lave_max 2.0 Local average cutoff
> (relative value), any pixel value above that will be considered as
> ice/aggregation/carbon etc.
> 02912: --lave_min -1.0 Local average cutoff
> (relative value), any pixel value below that will be considered as
> ice/aggregation/carbon etc.
> 02913: For 'black' cryoEM
> micrograph, set this to very small value e.g. -10.0 will not reject any
> 'black' dots in general.
> 02914: --lp 30 Low-pass filter to increase
> the contrast of raw micrographs, suggested range 20~50Å. This low-pass is
> after ice/aggregation detection.
> 02915: --hp 1000 High-pass filter to get rid
> of the global background of raw micrographs, suggested range 200~2000Å.
> This high-pass is after ice/aggregation detection.
> 02916: --do_pre_filter Specify to get rid of
> severely gradient background before ice/aggregation/carbon detection. This
> is not normally suggested because it might affect ice/carbon detection.
> 02917: --pre_lp 8.0 The same as --lp, but before
> the ice/contamination detection, might be better in severely gradient ice.
> 02918: Does not matter to use both
> --lp and --pre_lp, but suggested to use much smaller --pre_lp for better
> ice/contamination detection.
> 02919: --pre_hp 1000 The same as --hp, but before
> the ice/contamination detection, might be better in severely gradient ice.
> 02920: Otherwise, do not use
> --pre_hp or use a very big value.
> 02921: --detect_ice 1 Specify 0 to avoid
> ice/aggregation/carbon detection.
> 02922: --T_norm_type 1 Specify the type of Template
> normalization, 1, 2 or 3 allowed.
> 02923: --do_bandpass 1 Specify 0 to skip the
> bandpass; By default it will do bandpass filter.
> 02924: CTF options(not effective in this verion):
> 02925: --do_ctf Specify this option to do
> CTF determination and correction for better picking
> 02926: --do_local_ctf Specify this option to do
> local CTF determination and correction for each picked particle
> 02927: --kV 300 High tension in Kilovolt,
> typically 300, 200 or 120
> 02928: --cs 2.7 Spherical aberration, in
> millimeter
> 02929: --ac 0.1 Amplitude contrast; normal
> range 0.04~0.1; pure ice 0.04, carbon 0.1; but doesn't matter too much if
> using wrong value
> 02930:
> 02931: I/O options:
> 02932: --write_ccmax_mic Specify to write out
> cross-correlation files, in MRC stack
> 02933: --write_pf_mic Specify to write out
> phase-flipped(pf) micrographs(mic)
> 02934: --write_pref_mic Specify to write out
> pre-filted(pref) micrographs(mic)
> 02935: --write_bg_mic Specify to write out
> estimated background(bg) of the micrographs(mic)
> 02936: --write_bgfree_mic Specify to write out
> background subtracted (bgfree) micrographs(mic)
> 02937: --write_lsigma_mic Specify to write out local
> sigma (lsigma) micrographs(mic)
> 02938: --write_mic_mask Specify to write out the
> auto-detected mask (ice, contamination, aggregation, carbon edge etc.) by
> --lsigma_cutoff or --lave_max or --lave_max
> 02939: --exclusive_picking Specify to pick the
> particles by pre-defined coordinates that will be excluded.
> 02940: This is useful, when you
> have done 2D classification and provide the rubbish particles that
> Gautomatch will automatically exclude
> 02941: --excluded_suffix The suffix of coordinates to
> be excluded. Relion .star and EMAN .box file are both accepted, extended
> .box file format in Gautomach preferred.
> 02942: For example, if
> --excluded_suffix _rubbish.box is provided for mic0002.mrc, then Gautomatch
> will try to find mic0002_rubbish.box and exclude them during picking.
> 02943: --mask_excluded Specify this option to mask
> out the excluded coordinates so that it will nerve be taken into account in
> any step of processing, even not in the normalization step.
> 02944: This is helpful if the
> artifacts are extremely different from normal area of the micrographs.
> 02945: --global_excluded_box NONE Provide a coordinate
> .box/.star file to exclude these special coordinates completely from all
> micrographs before any processing.
> 02946: So generally, these area
> will not involve in normalization, ice/aggregation/carbon detection. They
> are completely gone.
> 02947: Note, the --excluded_suffix
> option is used for individual files.
> 02948: --do_unfinished Specify to autopick the
> unfinished micrographs
> 02949: --dont_invertT Whether to invert template
> contrast. VERY IMPORTANT!!! By default, the program will invert the 'white'
> templates to 'black' before picking.
> 02950: specify this option to avoid
> contrast inversion if the micrographs and templates have the same contrast
> 02951: --extract_raw Specify to extract particle
> from raw micrograph
> 02952: --extract_pf Specify to extract particle
> from phase-flipped micrograph; will write a new stack and will not
> overwrite raw particle stack
> 02953: --gid 0 GPU id, normally it's 0, use
> gpu_info to get information of all available GPUs.
> 02954:
> 02955: Example:
> 02956:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.58 --diameter 300 Micrographs/Falcon*.mrc (auto-generated
> templates for 'black' cryoEM micrograph)
> 02957:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 2.16
> Micrographs/Falcon*.mrc (for 'white' templates and 'black' micrograph
> 02958:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 3.2
> --dont_invertT Micrographs/Falcon*.mrc (for 'black' templates and 'black'
> micrograph)
> 02959:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> --apixM 1.08 --diameter 300 --boxsize 360 --write_bgfree_mic
> --write_lsigma_mic --extract_raw --write_ccmax Micrographs/Falcon*.mrc
> (suggested for manual diagnosis using the different types of output
> micrographs)
> 02960:
> /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> test?.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T
> templates_lp40_3.2A.mrcs --write_pref_mic --lsigma_cutoff 1.2 --cc_cutoff
> 0.18 --lave_D 80 --lave_min -0.8 --lave_max 1.2 --exclusive_picking
> --excluded_suffix _rubbish.star --mask_excluded --write_ccmax_mic
> --write_pf_mic --write_pref_mic --write_bg_mic --write_bgfree_mic
> --write_lsigma_mic --write_mic_mask --extract_raw --do_pre_filter 1
> --pre_lp 10 --pre_hp 1000 --lp 40 --boxsize 432
> 02961: --help Print full help document
> 02962: Error in function gautomatch_help_exit(), file automatch56.cu on
> line 1322: Failed to find any usable GPU device!! Exit now!
> 02963: Traceback (most recent call last):
> 02964: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 151,
> in run
> 02965: self.step._run() # not self.step.run() , to avoid race
> conditions
> 02966: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 237,
> in _run
> 02967: resultFiles = self._runFunc()
> 02968: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 233,
> in _runFunc
> 02969: return self._func(*self._args)
> 02970: File
> "/services/tools/scipion/2.0.0/pyworkflow/em/protocol/protocol_particles_picking.py",
> line 242, in pickMicrographStep
> 02971: self._pickMicrograph(mic, *args)
> 02972: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py",
> line 327, in _pickMicrograph
> 02973: self._pickMicrographList([mic], args)
> 02974: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py",
> line 355, in _pickMicrographList
> 02975: runJob=self.runJob)
> 02976: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/__init__.py",
> line 104, in runGautomatch
> 02977: runJob(cls.getProgram(), args, env=environ)
> 02978: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 1311,
> in runJob
> 02979: self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 02980: File
> "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 70,
> in runJob
> 02981: env=env, cwd=cwd, gpuList=self.getGpuList())
> 02982: File
> "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 52, in
> runJob
> 02983: return runCommand(command, env, cwd)
> 02984: File
> "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 67, in
> runCommand
> 02985: env=env, cwd=cwd)
> 02986: File
> "/services/tools/scipion/2.0.0/software/lib/python2.7/subprocess.py", line
> 190, in check_call
> 02987: raise CalledProcessError(retcode, cmd)
> 02988: CalledProcessError: Command
> '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0
> Runs/002849_ProtGautomatch/tmp/mic_000031/*.mrc -T
> Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5
> --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30
> --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit
> status 1
> 02989: ------------------- PROTOCOL FAILED (DONE 2/3526)
>
>
>
> Best wishes,
>
>
>
> Mar
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Maria D. M. P. R. <mar...@cp...> - 2020-06-16 09:14:44
|
Dear Scipion team,
I am trying to run Gautomatch v0.56 in Scipion (v2.0 Diocletian) and I have this issue (see below).
My question is what’s it going on? And if is it related with our CUDA version? We have CUDA version 10.0.130 and GPU Cuda version 10.2.
If I add GAUTOMATCH_CUDA_LIB variable to the config file with the path where CUDA10 is, I have the same issue.
Is there any CUDA10 version for Scipion?
Thank you so much for your help!
02662: STARTED: pickMicrographStep, step 28
02663: 2020-06-16 10:08:18.670414
02664: Picking micrograph: Runs/000388_ProtRelionMotioncor/extra/FoilHole_18276562_Data_18277147_18277148_20190719_1447_Fractions_aligned_mic_DW.mrc
02665: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 Runs/002849_ProtGautomatch/tmp/mic_000029/*.mrc -T Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5 --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30 --detect_ice 1 --T_norm_type 1 --do_bandpass 1
02666: ***************************************************************************************************
02667: Version: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 v0.56, updated on 2017-07-30
02668: Author: Kai Zhang@MRC Laboratory of Molecular Biology
02669: Contact: kz...@mr...
02670: Description: This is a GPU accelerated program for fully automatic particle picking.
02671: Note: Still under development, to be released soon ...
02672: ***************************************************************************************************
02673: Usage:
02674: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 [options] <micrographs>
02675:
02676: Options:
02677: Basic options: default values, description:
02678: --apixM 1.34 Pixel size of the micrograph, in angstrom
02679: --diameter 400 Particle diameter, in angstrom;
02680: --T NONE Particle picking templates in 2D MRC stack; must provide the correct pixel size if not the same as micrograph; auto-generated if not provided;
02681: --apixT 1.34 Pixel size of the templates, in angstrom; will be the same as --apixM if not set.
02682:
02683: Additional options(not suggested, only try to optimize in difficult cases), default values and description:
02684: --ang_step 5 Angular step size for picking, invalid for auto-templates
02685: --speed 2 Speed level {0,1,2,3,4}, the bigger the faster, but less accurate.
02686: --boxsize 128 Box size, in pixel, NOT in angstrom; a suggested value will be automatically calculated by --diameter and --apixM
02687: --min_dist 300 Minimum distance between particles in angstrom; 0.9~1.1X diameter; can be 0.3~0.5 for filament-like particle
02688: --cc_cutoff 0.1 Cross-correlation cutoff, 0.2~0.4 normally; Try to select several typical micrographs to optimize this value.
02689: Alternatively, it will be even faster if you use a small value, e.g. 0.1, first and then use 'box_filter.com' or 'box_filter2rl.com' to filter the box files afterwards.
02690: --lsigma_D 200 Diameter for estimation of local sigma, in angstrom
02691: --lsigma_cutoff 1.3 Local sigma cutoff (relative value), 1.2~1.5 should be a good range; normally a value >1.2 will be ice, protein aggregation or contamination
02692: --lave_D 400 Diameter for estimation of local average, in angstrom, 0.5~2.0X particle diameter suggested;
02693: However, if you have 'sharp'/'small' ice or any 'dark'/'bright' dots, use a smaller value will be much better to get rid of these areas.
02694: --lave_max 2.0 Local average cutoff (relative value), any pixel value above that will be considered as ice/aggregation/carbon etc.
02695: --lave_min -1.0 Local average cutoff (relative value), any pixel value below that will be considered as ice/aggregation/carbon etc.
02696: For 'black' cryoEM micrograph, set this to very small value e.g. -10.0 will not reject any 'black' dots in general.
02697: --lp 30 Low-pass filter to increase the contrast of raw micrographs, suggested range 20~50Å. This low-pass is after ice/aggregation detection.
02698: --hp 1000 High-pass filter to get rid of the global background of raw micrographs, suggested range 200~2000Å. This high-pass is after ice/aggregation detection.
02699: --do_pre_filter Specify to get rid of severely gradient background before ice/aggregation/carbon detection. This is not normally suggested because it might affect ice/carbon detection.
02700: --pre_lp 8.0 The same as --lp, but before the ice/contamination detection, might be better in severely gradient ice.
02701: Does not matter to use both --lp and --pre_lp, but suggested to use much smaller --pre_lp for better ice/contamination detection.
02702: --pre_hp 1000 The same as --hp, but before the ice/contamination detection, might be better in severely gradient ice.
02703: Otherwise, do not use --pre_hp or use a very big value.
02704: --detect_ice 1 Specify 0 to avoid ice/aggregation/carbon detection.
02705: --T_norm_type 1 Specify the type of Template normalization, 1, 2 or 3 allowed.
02706: --do_bandpass 1 Specify 0 to skip the bandpass; By default it will do bandpass filter.
02707: CTF options(not effective in this verion):
02708: --do_ctf Specify this option to do CTF determination and correction for better picking
02709: --do_local_ctf Specify this option to do local CTF determination and correction for each picked particle
02710: --kV 300 High tension in Kilovolt, typically 300, 200 or 120
02711: --cs 2.7 Spherical aberration, in millimeter
02712: --ac 0.1 Amplitude contrast; normal range 0.04~0.1; pure ice 0.04, carbon 0.1; but doesn't matter too much if using wrong value
02713:
02714: I/O options:
02715: --write_ccmax_mic Specify to write out cross-correlation files, in MRC stack
02716: --write_pf_mic Specify to write out phase-flipped(pf) micrographs(mic)
02717: --write_pref_mic Specify to write out pre-filted(pref) micrographs(mic)
02718: --write_bg_mic Specify to write out estimated background(bg) of the micrographs(mic)
02719: --write_bgfree_mic Specify to write out background subtracted (bgfree) micrographs(mic)
02720: --write_lsigma_mic Specify to write out local sigma (lsigma) micrographs(mic)
02721: --write_mic_mask Specify to write out the auto-detected mask (ice, contamination, aggregation, carbon edge etc.) by --lsigma_cutoff or --lave_max or --lave_max
02722: --exclusive_picking Specify to pick the particles by pre-defined coordinates that will be excluded.
02723: This is useful, when you have done 2D classification and provide the rubbish particles that Gautomatch will automatically exclude
02724: --excluded_suffix The suffix of coordinates to be excluded. Relion .star and EMAN .box file are both accepted, extended .box file format in Gautomach preferred.
02725: For example, if --excluded_suffix _rubbish.box is provided for mic0002.mrc, then Gautomatch will try to find mic0002_rubbish.box and exclude them during picking.
02726: --mask_excluded Specify this option to mask out the excluded coordinates so that it will nerve be taken into account in any step of processing, even not in the normalization step.
02727: This is helpful if the artifacts are extremely different from normal area of the micrographs.
02728: --global_excluded_box NONE Provide a coordinate .box/.star file to exclude these special coordinates completely from all micrographs before any processing.
02729: So generally, these area will not involve in normalization, ice/aggregation/carbon detection. They are completely gone.
02730: Note, the --excluded_suffix option is used for individual files.
02731: --do_unfinished Specify to autopick the unfinished micrographs
02732: --dont_invertT Whether to invert template contrast. VERY IMPORTANT!!! By default, the program will invert the 'white' templates to 'black' before picking.
02733: specify this option to avoid contrast inversion if the micrographs and templates have the same contrast
02734: --extract_raw Specify to extract particle from raw micrograph
02735: --extract_pf Specify to extract particle from phase-flipped micrograph; will write a new stack and will not overwrite raw particle stack
02736: --gid 0 GPU id, normally it's 0, use gpu_info to get information of all available GPUs.
02737:
02738: Example:
02739: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.58 --diameter 300 Micrographs/Falcon*.mrc (auto-generated templates for 'black' cryoEM micrograph)
02740: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 2.16 Micrographs/Falcon*.mrc (for 'white' templates and 'black' micrograph
02741: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 3.2 --dont_invertT Micrographs/Falcon*.mrc (for 'black' templates and 'black' micrograph)
02742: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 --boxsize 360 --write_bgfree_mic --write_lsigma_mic --extract_raw --write_ccmax Micrographs/Falcon*.mrc (suggested for manual diagnosis using the different types of output micrographs)
02743: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 test?.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T templates_lp40_3.2A.mrcs --write_pref_mic --lsigma_cutoff 1.2 --cc_cutoff 0.18 --lave_D 80 --lave_min -0.8 --lave_max 1.2 --exclusive_picking --excluded_suffix _rubbish.star --mask_excluded --write_ccmax_mic --write_pf_mic --write_pref_mic --write_bg_mic --write_bgfree_mic --write_lsigma_mic --write_mic_mask --extract_raw --do_pre_filter 1 --pre_lp 10 --pre_hp 1000 --lp 40 --boxsize 432
02744: --help Print full help document
02745: Error in function gautomatch_help_exit(), file automatch56.cu on line 1322: Failed to find any usable GPU device!! Exit now!
02746: Traceback (most recent call last):
02747: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 151, in run
02748: self.step._run() # not self.step.run() , to avoid race conditions
02749: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 237, in _run
02750: resultFiles = self._runFunc()
02751: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 233, in _runFunc
02752: return self._func(*self._args)
02753: File "/services/tools/scipion/2.0.0/pyworkflow/em/protocol/protocol_particles_picking.py", line 242, in pickMicrographStep
02754: self._pickMicrograph(mic, *args)
02755: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py", line 327, in _pickMicrograph
02756: self._pickMicrographList([mic], args)
02757: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py", line 355, in _pickMicrographList
02758: runJob=self.runJob)
02759: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/__init__.py", line 104, in runGautomatch
02760: runJob(cls.getProgram(), args, env=environ)
02761: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 1311, in runJob
02762: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
02763: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 70, in runJob
02764: env=env, cwd=cwd, gpuList=self.getGpuList())
02765: File "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 52, in runJob
02766: return runCommand(command, env, cwd)
02767: File "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 67, in runCommand
02768: env=env, cwd=cwd)
02769: File "/services/tools/scipion/2.0.0/software/lib/python2.7/subprocess.py", line 190, in check_call
02770: raise CalledProcessError(retcode, cmd)
02771: CalledProcessError: Command '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 Runs/002849_ProtGautomatch/tmp/mic_000027/*.mrc -T Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5 --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30 --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit status 1
02772: Picking micrograph: Runs/000388_ProtRelionMotioncor/extra/FoilHole_18276563_Data_18277114_18277115_20190719_1448_Fractions_aligned_mic_DW.mrc
02773: Protocol failed: Command '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 Runs/002849_ProtGautomatch/tmp/mic_000027/*.mrc -T Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5 --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30 --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit status 1
02774: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 Runs/002849_ProtGautomatch/tmp/mic_000031/*.mrc -T Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5 --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30 --detect_ice 1 --T_norm_type 1 --do_bandpass 1
02775: ***************************************************************************************************
02776: Version: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 v0.56, updated on 2017-07-30
02777: Author: Kai Zhang@MRC Laboratory of Molecular Biology
02778: Contact: kz...@mr...
02779: Description: This is a GPU accelerated program for fully automatic particle picking.
02780: Note: Still under development, to be released soon ...
02781: ***************************************************************************************************
02782: Usage:
02783: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 [options] <micrographs>
02784:
02785: Options:
02786: Basic options: default values, description:
02787: --apixM 1.34 Pixel size of the micrograph, in angstrom
02788: --diameter 400 Particle diameter, in angstrom;
02789: --T NONE Particle picking templates in 2D MRC stack; must provide the correct pixel size if not the same as micrograph; auto-generated if not provided;
02790: --apixT 1.34 Pixel size of the templates, in angstrom; will be the same as --apixM if not set.
02791:
02792: Additional options(not suggested, only try to optimize in difficult cases), default values and description:
02793: --ang_step 5 Angular step size for picking, invalid for auto-templates
02794: --speed 2 Speed level {0,1,2,3,4}, the bigger the faster, but less accurate.
02795: --boxsize 128 Box size, in pixel, NOT in angstrom; a suggested value will be automatically calculated by --diameter and --apixM
02796: --min_dist 300 Minimum distance between particles in angstrom; 0.9~1.1X diameter; can be 0.3~0.5 for filament-like particle
02797: --cc_cutoff 0.1 Cross-correlation cutoff, 0.2~0.4 normally; Try to select several typical micrographs to optimize this value.
02798: Alternatively, it will be even faster if you use a small value, e.g. 0.1, first and then use 'box_filter.com' or 'box_filter2rl.com' to filter the box files afterwards.
02799: --lsigma_D 200 Diameter for estimation of local sigma, in angstrom
02800: --lsigma_cutoff 1.3 Local sigma cutoff (relative value), 1.2~1.5 should be a good range; normally a value >1.2 will be ice, protein aggregation or contamination
02801: --lave_D 400 Diameter for estimation of local average, in angstrom, 0.5~2.0X particle diameter suggested;
02802: However, if you have 'sharp'/'small' ice or any 'dark'/'bright' dots, use a smaller value will be much better to get rid of these areas.
02803: --lave_max 2.0 Local average cutoff (relative value), any pixel value above that will be considered as ice/aggregation/carbon etc.
02804: --lave_min -1.0 Local average cutoff (relative value), any pixel value below that will be considered as ice/aggregation/carbon etc.
02805: For 'black' cryoEM micrograph, set this to very small value e.g. -10.0 will not reject any 'black' dots in general.
02806: --lp 30 Low-pass filter to increase the contrast of raw micrographs, suggested range 20~50Å. This low-pass is after ice/aggregation detection.
02807: --hp 1000 High-pass filter to get rid of the global background of raw micrographs, suggested range 200~2000Å. This high-pass is after ice/aggregation detection.
02808: --do_pre_filter Specify to get rid of severely gradient background before ice/aggregation/carbon detection. This is not normally suggested because it might affect ice/carbon detection.
02809: --pre_lp 8.0 The same as --lp, but before the ice/contamination detection, might be better in severely gradient ice.
02810: Does not matter to use both --lp and --pre_lp, but suggested to use much smaller --pre_lp for better ice/contamination detection.
02811: --pre_hp 1000 The same as --hp, but before the ice/contamination detection, might be better in severely gradient ice.
02812: Otherwise, do not use --pre_hp or use a very big value.
02813: --detect_ice 1 Specify 0 to avoid ice/aggregation/carbon detection.
02814: --T_norm_type 1 Specify the type of Template normalization, 1, 2 or 3 allowed.
02815: --do_bandpass 1 Specify 0 to skip the bandpass; By default it will do bandpass filter.
02816: CTF options(not effective in this verion):
02817: --do_ctf Specify this option to do CTF determination and correction for better picking
02818: --do_local_ctf Specify this option to do local CTF determination and correction for each picked particle
02819: --kV 300 High tension in Kilovolt, typically 300, 200 or 120
02820: --cs 2.7 Spherical aberration, in millimeter
02821: --ac 0.1 Amplitude contrast; normal range 0.04~0.1; pure ice 0.04, carbon 0.1; but doesn't matter too much if using wrong value
02822:
02823: I/O options:
02824: --write_ccmax_mic Specify to write out cross-correlation files, in MRC stack
02825: --write_pf_mic Specify to write out phase-flipped(pf) micrographs(mic)
02826: --write_pref_mic Specify to write out pre-filted(pref) micrographs(mic)
02827: --write_bg_mic Specify to write out estimated background(bg) of the micrographs(mic)
02828: --write_bgfree_mic Specify to write out background subtracted (bgfree) micrographs(mic)
02829: --write_lsigma_mic Specify to write out local sigma (lsigma) micrographs(mic)
02830: --write_mic_mask Specify to write out the auto-detected mask (ice, contamination, aggregation, carbon edge etc.) by --lsigma_cutoff or --lave_max or --lave_max
02831: --exclusive_picking Specify to pick the particles by pre-defined coordinates that will be excluded.
02832: This is useful, when you have done 2D classification and provide the rubbish particles that Gautomatch will automatically exclude
02833: --excluded_suffix The suffix of coordinates to be excluded. Relion .star and EMAN .box file are both accepted, extended .box file format in Gautomach preferred.
02834: For example, if --excluded_suffix _rubbish.box is provided for mic0002.mrc, then Gautomatch will try to find mic0002_rubbish.box and exclude them during picking.
02835: --mask_excluded Specify this option to mask out the excluded coordinates so that it will nerve be taken into account in any step of processing, even not in the normalization step.
02836: This is helpful if the artifacts are extremely different from normal area of the micrographs.
02837: --global_excluded_box NONE Provide a coordinate .box/.star file to exclude these special coordinates completely from all micrographs before any processing.
02838: So generally, these area will not involve in normalization, ice/aggregation/carbon detection. They are completely gone.
02839: Note, the --excluded_suffix option is used for individual files.
02840: --do_unfinished Specify to autopick the unfinished micrographs
02841: --dont_invertT Whether to invert template contrast. VERY IMPORTANT!!! By default, the program will invert the 'white' templates to 'black' before picking.
02842: specify this option to avoid contrast inversion if the micrographs and templates have the same contrast
02843: --extract_raw Specify to extract particle from raw micrograph
02844: --extract_pf Specify to extract particle from phase-flipped micrograph; will write a new stack and will not overwrite raw particle stack
02845: --gid 0 GPU id, normally it's 0, use gpu_info to get information of all available GPUs.
02846:
02847: Example:
02848: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.58 --diameter 300 Micrographs/Falcon*.mrc (auto-generated templates for 'black' cryoEM micrograph)
02849: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 2.16 Micrographs/Falcon*.mrc (for 'white' templates and 'black' micrograph
02850: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 3.2 --dont_invertT Micrographs/Falcon*.mrc (for 'black' templates and 'black' micrograph)
02851: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 --boxsize 360 --write_bgfree_mic --write_lsigma_mic --extract_raw --write_ccmax Micrographs/Falcon*.mrc (suggested for manual diagnosis using the different types of output micrographs)
02852: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 test?.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T templates_lp40_3.2A.mrcs --write_pref_mic --lsigma_cutoff 1.2 --cc_cutoff 0.18 --lave_D 80 --lave_min -0.8 --lave_max 1.2 --exclusive_picking --excluded_suffix _rubbish.star --mask_excluded --write_ccmax_mic --write_pf_mic --write_pref_mic --write_bg_mic --write_bgfree_mic --write_lsigma_mic --write_mic_mask --extract_raw --do_pre_filter 1 --pre_lp 10 --pre_hp 1000 --lp 40 --boxsize 432
02853: --help Print full help document
02854: Error in function gautomatch_help_exit(), file automatch56.cu on line 1322: Failed to find any usable GPU device!! Exit now!
02855: Traceback (most recent call last):
02856: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 151, in run
02857: self.step._run() # not self.step.run() , to avoid race conditions
02858: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 237, in _run
02859: resultFiles = self._runFunc()
02860: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 233, in _runFunc
02861: return self._func(*self._args)
02862: File "/services/tools/scipion/2.0.0/pyworkflow/em/protocol/protocol_particles_picking.py", line 242, in pickMicrographStep
02863: self._pickMicrograph(mic, *args)
02864: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py", line 327, in _pickMicrograph
02865: self._pickMicrographList([mic], args)
02866: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py", line 355, in _pickMicrographList
02867: runJob=self.runJob)
02868: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/__init__.py", line 104, in runGautomatch
02869: runJob(cls.getProgram(), args, env=environ)
02870: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 1311, in runJob
02871: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
02872: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 70, in runJob
02873: env=env, cwd=cwd, gpuList=self.getGpuList())
02874: File "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 52, in runJob
02875: return runCommand(command, env, cwd)
02876: File "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 67, in runCommand
02877: env=env, cwd=cwd)
02878: File "/services/tools/scipion/2.0.0/software/lib/python2.7/subprocess.py", line 190, in check_call
02879: raise CalledProcessError(retcode, cmd)
02880: CalledProcessError: Command '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 Runs/002849_ProtGautomatch/tmp/mic_000029/*.mrc -T Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5 --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30 --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit status 1
02881: FAILED: pickMicrographStep, step 26
02882: 2020-06-16 10:08:18.699681
02883: ***************************************************************************************************
02884: Version: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 v0.56, updated on 2017-07-30
02885: Author: Kai Zhang@MRC Laboratory of Molecular Biology
02886: Contact: kz...@mr...
02887: Description: This is a GPU accelerated program for fully automatic particle picking.
02888: Note: Still under development, to be released soon ...
02889: ***************************************************************************************************
02890: Usage:
02891: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 [options] <micrographs>
02892:
02893: Options:
02894: Basic options: default values, description:
02895: --apixM 1.34 Pixel size of the micrograph, in angstrom
02896: --diameter 400 Particle diameter, in angstrom;
02897: --T NONE Particle picking templates in 2D MRC stack; must provide the correct pixel size if not the same as micrograph; auto-generated if not provided;
02898: --apixT 1.34 Pixel size of the templates, in angstrom; will be the same as --apixM if not set.
02899:
02900: Additional options(not suggested, only try to optimize in difficult cases), default values and description:
02901: --ang_step 5 Angular step size for picking, invalid for auto-templates
02902: --speed 2 Speed level {0,1,2,3,4}, the bigger the faster, but less accurate.
02903: --boxsize 128 Box size, in pixel, NOT in angstrom; a suggested value will be automatically calculated by --diameter and --apixM
02904: --min_dist 300 Minimum distance between particles in angstrom; 0.9~1.1X diameter; can be 0.3~0.5 for filament-like particle
02905: --cc_cutoff 0.1 Cross-correlation cutoff, 0.2~0.4 normally; Try to select several typical micrographs to optimize this value.
02906: Alternatively, it will be even faster if you use a small value, e.g. 0.1, first and then use 'box_filter.com' or 'box_filter2rl.com' to filter the box files afterwards.
02907: --lsigma_D 200 Diameter for estimation of local sigma, in angstrom
02908: --lsigma_cutoff 1.3 Local sigma cutoff (relative value), 1.2~1.5 should be a good range; normally a value >1.2 will be ice, protein aggregation or contamination
02909: --lave_D 400 Diameter for estimation of local average, in angstrom, 0.5~2.0X particle diameter suggested;
02910: However, if you have 'sharp'/'small' ice or any 'dark'/'bright' dots, use a smaller value will be much better to get rid of these areas.
02911: --lave_max 2.0 Local average cutoff (relative value), any pixel value above that will be considered as ice/aggregation/carbon etc.
02912: --lave_min -1.0 Local average cutoff (relative value), any pixel value below that will be considered as ice/aggregation/carbon etc.
02913: For 'black' cryoEM micrograph, set this to very small value e.g. -10.0 will not reject any 'black' dots in general.
02914: --lp 30 Low-pass filter to increase the contrast of raw micrographs, suggested range 20~50Å. This low-pass is after ice/aggregation detection.
02915: --hp 1000 High-pass filter to get rid of the global background of raw micrographs, suggested range 200~2000Å. This high-pass is after ice/aggregation detection.
02916: --do_pre_filter Specify to get rid of severely gradient background before ice/aggregation/carbon detection. This is not normally suggested because it might affect ice/carbon detection.
02917: --pre_lp 8.0 The same as --lp, but before the ice/contamination detection, might be better in severely gradient ice.
02918: Does not matter to use both --lp and --pre_lp, but suggested to use much smaller --pre_lp for better ice/contamination detection.
02919: --pre_hp 1000 The same as --hp, but before the ice/contamination detection, might be better in severely gradient ice.
02920: Otherwise, do not use --pre_hp or use a very big value.
02921: --detect_ice 1 Specify 0 to avoid ice/aggregation/carbon detection.
02922: --T_norm_type 1 Specify the type of Template normalization, 1, 2 or 3 allowed.
02923: --do_bandpass 1 Specify 0 to skip the bandpass; By default it will do bandpass filter.
02924: CTF options(not effective in this verion):
02925: --do_ctf Specify this option to do CTF determination and correction for better picking
02926: --do_local_ctf Specify this option to do local CTF determination and correction for each picked particle
02927: --kV 300 High tension in Kilovolt, typically 300, 200 or 120
02928: --cs 2.7 Spherical aberration, in millimeter
02929: --ac 0.1 Amplitude contrast; normal range 0.04~0.1; pure ice 0.04, carbon 0.1; but doesn't matter too much if using wrong value
02930:
02931: I/O options:
02932: --write_ccmax_mic Specify to write out cross-correlation files, in MRC stack
02933: --write_pf_mic Specify to write out phase-flipped(pf) micrographs(mic)
02934: --write_pref_mic Specify to write out pre-filted(pref) micrographs(mic)
02935: --write_bg_mic Specify to write out estimated background(bg) of the micrographs(mic)
02936: --write_bgfree_mic Specify to write out background subtracted (bgfree) micrographs(mic)
02937: --write_lsigma_mic Specify to write out local sigma (lsigma) micrographs(mic)
02938: --write_mic_mask Specify to write out the auto-detected mask (ice, contamination, aggregation, carbon edge etc.) by --lsigma_cutoff or --lave_max or --lave_max
02939: --exclusive_picking Specify to pick the particles by pre-defined coordinates that will be excluded.
02940: This is useful, when you have done 2D classification and provide the rubbish particles that Gautomatch will automatically exclude
02941: --excluded_suffix The suffix of coordinates to be excluded. Relion .star and EMAN .box file are both accepted, extended .box file format in Gautomach preferred.
02942: For example, if --excluded_suffix _rubbish.box is provided for mic0002.mrc, then Gautomatch will try to find mic0002_rubbish.box and exclude them during picking.
02943: --mask_excluded Specify this option to mask out the excluded coordinates so that it will nerve be taken into account in any step of processing, even not in the normalization step.
02944: This is helpful if the artifacts are extremely different from normal area of the micrographs.
02945: --global_excluded_box NONE Provide a coordinate .box/.star file to exclude these special coordinates completely from all micrographs before any processing.
02946: So generally, these area will not involve in normalization, ice/aggregation/carbon detection. They are completely gone.
02947: Note, the --excluded_suffix option is used for individual files.
02948: --do_unfinished Specify to autopick the unfinished micrographs
02949: --dont_invertT Whether to invert template contrast. VERY IMPORTANT!!! By default, the program will invert the 'white' templates to 'black' before picking.
02950: specify this option to avoid contrast inversion if the micrographs and templates have the same contrast
02951: --extract_raw Specify to extract particle from raw micrograph
02952: --extract_pf Specify to extract particle from phase-flipped micrograph; will write a new stack and will not overwrite raw particle stack
02953: --gid 0 GPU id, normally it's 0, use gpu_info to get information of all available GPUs.
02954:
02955: Example:
02956: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.58 --diameter 300 Micrographs/Falcon*.mrc (auto-generated templates for 'black' cryoEM micrograph)
02957: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 2.16 Micrographs/Falcon*.mrc (for 'white' templates and 'black' micrograph
02958: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 -T templates.mrcs --apixT 3.2 --dont_invertT Micrographs/Falcon*.mrc (for 'black' templates and 'black' micrograph)
02959: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 --apixM 1.08 --diameter 300 --boxsize 360 --write_bgfree_mic --write_lsigma_mic --extract_raw --write_ccmax Micrographs/Falcon*.mrc (suggested for manual diagnosis using the different types of output micrographs)
02960: /services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 test?.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T templates_lp40_3.2A.mrcs --write_pref_mic --lsigma_cutoff 1.2 --cc_cutoff 0.18 --lave_D 80 --lave_min -0.8 --lave_max 1.2 --exclusive_picking --excluded_suffix _rubbish.star --mask_excluded --write_ccmax_mic --write_pf_mic --write_pref_mic --write_bg_mic --write_bgfree_mic --write_lsigma_mic --write_mic_mask --extract_raw --do_pre_filter 1 --pre_lp 10 --pre_hp 1000 --lp 40 --boxsize 432
02961: --help Print full help document
02962: Error in function gautomatch_help_exit(), file automatch56.cu on line 1322: Failed to find any usable GPU device!! Exit now!
02963: Traceback (most recent call last):
02964: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 151, in run
02965: self.step._run() # not self.step.run() , to avoid race conditions
02966: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 237, in _run
02967: resultFiles = self._runFunc()
02968: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 233, in _runFunc
02969: return self._func(*self._args)
02970: File "/services/tools/scipion/2.0.0/pyworkflow/em/protocol/protocol_particles_picking.py", line 242, in pickMicrographStep
02971: self._pickMicrograph(mic, *args)
02972: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py", line 327, in _pickMicrograph
02973: self._pickMicrographList([mic], args)
02974: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/protocols/protocol_gautomatch.py", line 355, in _pickMicrographList
02975: runJob=self.runJob)
02976: File "/services/tools/scipion/2.0.0/software/lib/python2.7/site-packages/gautomatch/__init__.py", line 104, in runGautomatch
02977: runJob(cls.getProgram(), args, env=environ)
02978: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/protocol.py", line 1311, in runJob
02979: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
02980: File "/services/tools/scipion/2.0.0/pyworkflow/protocol/executor.py", line 70, in runJob
02981: env=env, cwd=cwd, gpuList=self.getGpuList())
02982: File "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 52, in runJob
02983: return runCommand(command, env, cwd)
02984: File "/services/tools/scipion/2.0.0/pyworkflow/utils/process.py", line 67, in runCommand
02985: env=env, cwd=cwd)
02986: File "/services/tools/scipion/2.0.0/software/lib/python2.7/subprocess.py", line 190, in check_call
02987: raise CalledProcessError(retcode, cmd)
02988: CalledProcessError: Command '/services/tools/scipion/2.0.0/software/em/gautomatch-0.56/bin/Gautomatch_v0.56_sm60_cu8.0 Runs/002849_ProtGautomatch/tmp/mic_000031/*.mrc -T Runs/002849_ProtGautomatch/extra/references.mrcs --apixM 1.10 --ang_step 5 --diameter 408 --lp 30 --hp 1000 --gid 0 --apixT 1.10 --cc_cutoff 0.30 --detect_ice 1 --T_norm_type 1 --do_bandpass 1' returned non-zero exit status 1
02989: ------------------- PROTOCOL FAILED (DONE 2/3526)
Best wishes,
Mar
|
|
From: <pc...@cn...> - 2020-06-11 05:01:56
|
<div dir='auto'><div dir="auto">Could you please resend files with the errors <div dir="auto"><br></div><div dir="auto"><br></div></div><div><br><div class="elided-text">El 9 jun. 2020 16:24, Grigory Sharov <sha...@gm...> escribió:<br type="attribution"><blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Dmitry,<div><br></div><div>Though I am not the maintainer of the sphire plugin and unfortunately I don't have scipion 2.0 at the moment, I couldn't reproduce this with the newer release of cryolo / scipion 3. Installation error you have can be ignored afaik, since you cant fix it without updating the cryolo binary. The run error you have says missing config.json file. Can you check if this file is missing in the extra folder of the protocol run? </div><div><br clear="all"><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">Best regards,<br>Grigory</span></font></div><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt"><br></span></font></div><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">--------------------------------------------------------------------------------</span></font></div><div style="color:rgb( 0 , 0 , 0 )"><span style="font-size:12.8px">Grigory Sharov, Ph.D.</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">MRC Laboratory of Molecular Biology,</span><br style="font-size:12.8px"><span style="font-size:12.8px">Francis Crick Avenue,</span><br style="font-size:12.8px"><span style="font-size:12.8px">Cambridge Biomedical Campus,</span><br style="font-size:12.8px"><span style="font-size:12.8px">Cambridge CB2 0QH, UK.</span><br style="font-size:12.8px"><span style="font-size:12.8px">tel. </span><a href="tel:+44%201223%20267228" style="color:rgb( 17 , 85 , 204 );font-size:12.8px">+44 (0) 1223 267228</a></div><div style="color:rgb( 0 , 0 , 0 )"><span style="font-size:12.8px">e-mail: </span><a href="mailto:gs...@mr..." style="color:rgb( 17 , 85 , 204 );font-size:12.8px">gs...@mr...</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="elided-text"><div dir="ltr">On Tue, Jun 9, 2020 at 1:35 PM Dmitry Semchonok <<a href="mailto:Sem...@gm...">Sem...@gm...</a>> wrote:<br></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"><br> <br> <br> <br> Dear Grigory,<br> <br> We followed your suggestions to make the sphire work. <br> <br> The problem appeared to be in the initial sphire plugin installation. <br> So we decided to re-install the sphire.<br> <br> During installation we got the error - please see the files attached.<br> <br> Could you please suggest how could we fix it?<br> <br> <br> <br> <br> Thank you!<br> <br> Sincerely,<br> Dmitry<br> <br> <br> </blockquote></div> </blockquote></div><br></div></div> |
|
From: Grigory S. <sha...@gm...> - 2020-06-09 15:35:13
|
I was able to run sphire plugin 1.4.0 and cryolo 1.6.1 in scipion 2 now with no errors. I ran training with fine tuning of either general or input model and got no errors with json config file. Unless /usr/local/bin/startEMAN2scipion does something weird I don't see any other solutions. 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, Jun 9, 2020 at 3:41 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > Thank you! > > Yes, the file is there. > > > > > Sincerely, > > Dmitry > > > > > > On 9. Jun 2020, at 16:24, Grigory Sharov <sha...@gm...> wrote: > > Hi Dmitry, > > Though I am not the maintainer of the sphire plugin and unfortunately I > don't have scipion 2.0 at the moment, I couldn't reproduce this with the > newer release of cryolo / scipion 3. Installation error you have can be > ignored afaik, since you cant fix it without updating the cryolo binary. > The run error you have says missing config.json file. Can you check if this > file is missing in the extra folder of the protocol run? > > 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, Jun 9, 2020 at 1:35 PM Dmitry Semchonok <Sem...@gm...> > wrote: > >> >> >> >> >> Dear Grigory, >> >> We followed your suggestions to make the sphire work. >> >> The problem appeared to be in the initial sphire plugin installation. >> So we decided to re-install the sphire. >> >> During installation we got the error - please see the files attached. >> >> Could you please suggest how could we fix it? >> >> >> >> >> Thank you! >> >> Sincerely, >> Dmitry >> >> >> > |
|
From: Dmitry S. <Sem...@gm...> - 2020-06-09 14:41:33
|
Dear Grigory, Thank you! Yes, the file is there. Sincerely, Dmitry > On 9. Jun 2020, at 16:24, Grigory Sharov <sha...@gm...> wrote: > > Hi Dmitry, > > Though I am not the maintainer of the sphire plugin and unfortunately I don't have scipion 2.0 at the moment, I couldn't reproduce this with the newer release of cryolo / scipion 3. Installation error you have can be ignored afaik, since you cant fix it without updating the cryolo binary. The run error you have says missing config.json file. Can you check if this file is missing in the extra folder of the protocol run? > > 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 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Tue, Jun 9, 2020 at 1:35 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > > > > > Dear Grigory, > > We followed your suggestions to make the sphire work. > > The problem appeared to be in the initial sphire plugin installation. > So we decided to re-install the sphire. > > During installation we got the error - please see the files attached. > > Could you please suggest how could we fix it? > > > > > Thank you! > > Sincerely, > Dmitry > > |
|
From: Grigory S. <sha...@gm...> - 2020-06-09 14:25:30
|
Hi Dmitry, Though I am not the maintainer of the sphire plugin and unfortunately I don't have scipion 2.0 at the moment, I couldn't reproduce this with the newer release of cryolo / scipion 3. Installation error you have can be ignored afaik, since you cant fix it without updating the cryolo binary. The run error you have says missing config.json file. Can you check if this file is missing in the extra folder of the protocol run? 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, Jun 9, 2020 at 1:35 PM Dmitry Semchonok <Sem...@gm...> wrote: > > > > > Dear Grigory, > > We followed your suggestions to make the sphire work. > > The problem appeared to be in the initial sphire plugin installation. > So we decided to re-install the sphire. > > During installation we got the error - please see the files attached. > > Could you please suggest how could we fix it? > > > > > Thank you! > > Sincerely, > Dmitry > > > |
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From: Dmitry A. S. <sem...@gm...> - 2020-06-08 12:07:24
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Dear Wolfgang, Thanks a lot! I will try that. Sincerely, Dmitry ------ Original Message ------ From: "Lugmayr, Wolfgang" <w.l...@uk...> To: "Mailing list for Scipion users" <sci...@li...> Sent: 08-Jun-20 1:27:05 PM Subject: Re: [scipion-users] shire cryo training protocol failed from running >hi dmitry, > >we use a cryolo installation outside of scipion and added the following >lines to the config/scipion.conf > >CONDA_ACTIVATION_CMD = source >/beegfs/cssb/software/anaconda3/etc/profile.d/conda.sh >CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7 > >cheers, >wolfgang > > >-------------------------------------------------------------------------------- >From: "Grigory Sharov" <sha...@gm...> >To: "Mailing list for Scipion users" ><sci...@li...> >Sent: Thursday, 4 June, 2020 14:54:20 >Subject: Re: [scipion-users] shire cryo training protocol failed from >running > >Hi Dmitry, > >Here is the error message: > >2020-06-04 14:19:55.483884 >00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying >on conda being in the PATH >00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json >-w 5 -g 0 -e 10 --fine_tune >00024: /bin/sh: conda: command not found > >You need to have conda command in your path or define the variable as >it says > >Grigory. > > >On Thu, Jun 4, 2020, 13:40 Dmitry Semchonok <Sem...@gm...> >wrote: >>Dear colleagues, >> >>I have a problems running shire cryo training protocol in SCIPION. >> >>Do you know how to fix it? >> >> >>Thank you! >> >>Sincerely, >>Dmitry >> >> >> >>============== >>RUNSTDOUT >>=============== >> >>UNNING PROTOCOL ----------------- >>00002: HostName: dataanalysisserver1 >>00003: PID: 69964 >>00004: Scipion: v2.0 (2019-04-23) Diocletian >>00005: currentDir: >>/home/user/Data/ScipionUserData/projects/Colette__03_06__20 >>00006: workingDir: Runs/000317_SphireProtCRYOLOTraining >>00007: runMode: Restart >>00008: MPI: 1 >>00009: threads: 1 >>00010: Starting at step: 1 >>00011: Running steps >>00012: STARTED: convertInputStep, step 1 >>00013: 2020-06-04 14:19:55.349748 >>00014: FINISHED: convertInputStep, step 1 >>00015: 2020-06-04 14:19:55.477612 >>00016: STARTED: createConfigStep, step 2 >>00017: 2020-06-04 14:19:55.480179 >>00018: FINISHED: createConfigStep, step 2 >>00019: 2020-06-04 14:19:55.481720 >>00020: STARTED: cryoloModelingStep, step 3 >>00021: 2020-06-04 14:19:55.483884 >>00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying >>on conda being in the PATH >>00023: conda activate cryolo-1.6.1 && cryolo_train.py -c >>config.json -w 5 -g 0 -e 10 --fine_tune >>00024: /bin/sh: conda: command not found >>00025: Traceback (most recent call last): >>00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 186, in run >>00027: self._run() >>00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 237, in _run >>00029: resultFiles = self._runFunc() >>00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 233, in _runFunc >>00031: return self._func(*self._args) >>00032: File >>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", >>line 246, in cryoloModelingStep >>00033: self.runCryoloTrain(5, extraArgs=extraArgs) >>00034: File >>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", >>line 243, in runCryoloTrain >>00035: cwd=self._getWorkDir()) >>00036: File >>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", >>line 220, in runCryolo >>00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), >>cwd=cwd) >>00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 1311, in runJob >>00039: self._stepsExecutor.runJob(self._log, program, arguments, >>**kwargs) >>00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", >>line 70, in runJob >>00041: env=env, cwd=cwd, gpuList=self.getGpuList()) >>00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line >>52, in runJob >>00043: return runCommand(command, env, cwd) >>00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line >>67, in runCommand >>00045: env=env, cwd=cwd) >>00046: File >>"/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, >>in check_call >>00047: raise CalledProcessError(retcode, cmd) >>00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && >>cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned >>non-zero exit status 127 >>00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && >>cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned >>non-zero exit status 127 >>00050: FAILED: cryoloModelingStep, step 3 >>00051: 2020-06-04 14:19:55.510445 >>00052: *** Last status is failed >>00053: ------------------- PROTOCOL FAILED (DONE 3/4) >> >>============================================================ >>======== >>RUN LOG >>======= >>RUNNING PROTOCOL ----------------- >>00002: HostName: dataanalysisserver1 >>00003: PID: 69964 >>00004: Scipion: v2.0 (2019-04-23) Diocletian >>00005: currentDir: >>/home/user/Data/ScipionUserData/projects/Colette__03_06__20 >>00006: workingDir: Runs/000317_SphireProtCRYOLOTraining >>00007: runMode: Restart >>00008: MPI: 1 >>00009: threads: 1 >>00010: Starting at step: 1 >>00011: Running steps >>00012: STARTED: convertInputStep, step 1 >>00013: 2020-06-04 14:19:55.349748 >>00014: FINISHED: convertInputStep, step 1 >>00015: 2020-06-04 14:19:55.477612 >>00016: STARTED: createConfigStep, step 2 >>00017: 2020-06-04 14:19:55.480179 >>00018: FINISHED: createConfigStep, step 2 >>00019: 2020-06-04 14:19:55.481720 >>00020: STARTED: cryoloModelingStep, step 3 >>00021: 2020-06-04 14:19:55.483884 >>00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying >>on conda being in the PATH >>00023: conda activate cryolo-1.6.1 && cryolo_train.py -c >>config.json -w 5 -g 0 -e 10 --fine_tune >>00024: /bin/sh: conda: command not found >>00025: Traceback (most recent call last): >>00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 186, in run >>00027: self._run() >>00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 237, in _run >>00029: resultFiles = self._runFunc() >>00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 233, in _runFunc >>00031: return self._func(*self._args) >>00032: File >>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", >>line 246, in cryoloModelingStep >>00033: self.runCryoloTrain(5, extraArgs=extraArgs) >>00034: File >>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", >>line 243, in runCryoloTrain >>00035: cwd=self._getWorkDir()) >>00036: File >>"/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", >>line 220, in runCryolo >>00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), >>cwd=cwd) >>00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", >>line 1311, in runJob >>00039: self._stepsExecutor.runJob(self._log, program, arguments, >>**kwargs) >>00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", >>line 70, in runJob >>00041: env=env, cwd=cwd, gpuList=self.getGpuList()) >>00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line >>52, in runJob >>00043: return runCommand(command, env, cwd) >>00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line >>67, in runCommand >>00045: env=env, cwd=cwd) >>00046: File >>"/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, >>in check_call >>00047: raise CalledProcessError(retcode, cmd) >>00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && >>cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned >>non-zero exit status 127 >>00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && >>cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned >>non-zero exit status 127 >>00050: FAILED: cryoloModelingStep, step 3 >>00051: 2020-06-04 14:19:55.510445 >>00052: *** Last status is failed >>00053: ------------------- PROTOCOL FAILED (DONE 3/4) >> >>_______________________________________________ >>scipion-users mailing list >>sci...@li... >>https://lists.sourceforge.net/lists/listinfo/scipion-users > > >_______________________________________________ >scipion-users mailing list >sci...@li... >https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Lugmayr, W. <w.l...@uk...> - 2020-06-08 11:27:20
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hi dmitry, we use a cryolo installation outside of scipion and added the following lines to the config/scipion.conf CONDA_ACTIVATION_CMD = source /beegfs/cssb/software/anaconda3/etc/profile.d/conda.sh CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7 cheers, wolfgang From: "Grigory Sharov" <sha...@gm...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Thursday, 4 June, 2020 14:54:20 Subject: Re: [scipion-users] shire cryo training protocol failed from running Hi Dmitry, Here is the error message: 2020-06-04 14:19:55.483884 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune 00024: /bin/sh: conda: command not found You need to have conda command in your path or define the variable as it says Grigory. On Thu, Jun 4, 2020, 13:40 Dmitry Semchonok < [ mailto:Sem...@gm... | Sem...@gm... ] > wrote: Dear colleagues, I have a problems running shire cryo training protocol in SCIPION. Do you know how to fix it? Thank you! Sincerely, Dmitry ============== RUNSTDOUT =============== UNNING PROTOCOL ----------------- 00002: HostName: dataanalysisserver1 00003: PID: 69964 00004: Scipion: v2.0 (2019-04-23) Diocletian 00005: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20 00006: workingDir: Runs/000317_SphireProtCRYOLOTraining 00007: runMode: Restart 00008: MPI: 1 00009: threads: 1 00010: Starting at step: 1 00011: Running steps 00012: STARTED: convertInputStep, step 1 00013: 2020-06-04 14:19:55.349748 00014: FINISHED: convertInputStep, step 1 00015: 2020-06-04 14:19:55.477612 00016: STARTED: createConfigStep, step 2 00017: 2020-06-04 14:19:55.480179 00018: FINISHED: createConfigStep, step 2 00019: 2020-06-04 14:19:55.481720 00020: STARTED: cryoloModelingStep, step 3 00021: 2020-06-04 14:19:55.483884 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune 00024: /bin/sh: conda: command not found 00025: Traceback (most recent call last): 00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in run 00027: self._run() 00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in _run 00029: resultFiles = self._runFunc() 00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc 00031: return self._func(*self._args) 00032: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 246, in cryoloModelingStep 00033: self.runCryoloTrain(5, extraArgs=extraArgs) 00034: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 243, in runCryoloTrain 00035: cwd=self._getWorkDir()) 00036: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", line 220, in runCryolo 00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd) 00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 1311, in runJob 00039: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", line 70, in runJob 00041: env=env, cwd=cwd, gpuList=self.getGpuList()) 00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line 52, in runJob 00043: return runCommand(command, env, cwd) 00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line 67, in runCommand 00045: env=env, cwd=cwd) 00046: File "/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, in check_call 00047: raise CalledProcessError(retcode, cmd) 00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00050: FAILED: cryoloModelingStep, step 3 00051: 2020-06-04 14:19:55.510445 00052: *** Last status is failed 00053: ------------------- PROTOCOL FAILED (DONE 3/4) ============================================================ ======== RUN LOG ======= RUNNING PROTOCOL ----------------- 00002: HostName: dataanalysisserver1 00003: PID: 69964 00004: Scipion: v2.0 (2019-04-23) Diocletian 00005: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20 00006: workingDir: Runs/000317_SphireProtCRYOLOTraining 00007: runMode: Restart 00008: MPI: 1 00009: threads: 1 00010: Starting at step: 1 00011: Running steps 00012: STARTED: convertInputStep, step 1 00013: 2020-06-04 14:19:55.349748 00014: FINISHED: convertInputStep, step 1 00015: 2020-06-04 14:19:55.477612 00016: STARTED: createConfigStep, step 2 00017: 2020-06-04 14:19:55.480179 00018: FINISHED: createConfigStep, step 2 00019: 2020-06-04 14:19:55.481720 00020: STARTED: cryoloModelingStep, step 3 00021: 2020-06-04 14:19:55.483884 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune 00024: /bin/sh: conda: command not found 00025: Traceback (most recent call last): 00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in run 00027: self._run() 00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in _run 00029: resultFiles = self._runFunc() 00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc 00031: return self._func(*self._args) 00032: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 246, in cryoloModelingStep 00033: self.runCryoloTrain(5, extraArgs=extraArgs) 00034: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 243, in runCryoloTrain 00035: cwd=self._getWorkDir()) 00036: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", line 220, in runCryolo 00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd) 00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 1311, in runJob 00039: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", line 70, in runJob 00041: env=env, cwd=cwd, gpuList=self.getGpuList()) 00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line 52, in runJob 00043: return runCommand(command, env, cwd) 00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line 67, in runCommand 00045: env=env, cwd=cwd) 00046: File "/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, in check_call 00047: raise CalledProcessError(retcode, cmd) 00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00050: FAILED: cryoloModelingStep, step 3 00051: 2020-06-04 14:19:55.510445 00052: *** Last status is failed 00053: ------------------- PROTOCOL FAILED (DONE 3/4) _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-06-04 12:54:39
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Hi Dmitry, Here is the error message: 2020-06-04 14:19:55.483884 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune 00024: /bin/sh: conda: command not found You need to have conda command in your path or define the variable as it says Grigory. On Thu, Jun 4, 2020, 13:40 Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > I have a problems running shire cryo training protocol in SCIPION. > > Do you know how to fix it? > > > Thank you! > > Sincerely, > Dmitry > > > > ============== > RUNSTDOUT > =============== > > UNNING PROTOCOL ----------------- > 00002: HostName: dataanalysisserver1 > 00003: PID: 69964 > 00004: Scipion: v2.0 (2019-04-23) Diocletian > 00005: currentDir: > /home/user/Data/ScipionUserData/projects/Colette__03_06__20 > 00006: workingDir: Runs/000317_SphireProtCRYOLOTraining > 00007: runMode: Restart > 00008: MPI: 1 > 00009: threads: 1 > 00010: Starting at step: 1 > 00011: Running steps > 00012: STARTED: convertInputStep, step 1 > 00013: 2020-06-04 14:19:55.349748 > 00014: FINISHED: convertInputStep, step 1 > 00015: 2020-06-04 14:19:55.477612 > 00016: STARTED: createConfigStep, step 2 > 00017: 2020-06-04 14:19:55.480179 > 00018: FINISHED: createConfigStep, step 2 > 00019: 2020-06-04 14:19:55.481720 > 00020: STARTED: cryoloModelingStep, step 3 > 00021: 2020-06-04 14:19:55.483884 > 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on > conda being in the PATH > 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w > 5 -g 0 -e 10 --fine_tune > 00024: /bin/sh: conda: command not found > 00025: Traceback (most recent call last): > 00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 186, in run > 00027: self._run() > 00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 237, in _run > 00029: resultFiles = self._runFunc() > 00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 233, in _runFunc > 00031: return self._func(*self._args) > 00032: File > "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", > line 246, in cryoloModelingStep > 00033: self.runCryoloTrain(5, extraArgs=extraArgs) > 00034: File > "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", > line 243, in runCryoloTrain > 00035: cwd=self._getWorkDir()) > 00036: File > "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", > line 220, in runCryolo > 00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), > cwd=cwd) > 00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 1311, in runJob > 00039: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > 00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", line > 70, in runJob > 00041: env=env, cwd=cwd, gpuList=self.getGpuList()) > 00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line 52, > in runJob > 00043: return runCommand(command, env, cwd) > 00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line 67, > in runCommand > 00045: env=env, cwd=cwd) > 00046: File "/usr/local/scipion/software/lib/python2.7/subprocess.py", > line 190, in check_call > 00047: raise CalledProcessError(retcode, cmd) > 00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && > cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned > non-zero exit status 127 > 00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && > cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned > non-zero exit status 127 > 00050: FAILED: cryoloModelingStep, step 3 > 00051: 2020-06-04 14:19:55.510445 > 00052: *** Last status is failed > 00053: ------------------- PROTOCOL FAILED (DONE 3/4) > > ============================================================ > ======== > RUN LOG > ======= > RUNNING PROTOCOL ----------------- > 00002: HostName: dataanalysisserver1 > 00003: PID: 69964 > 00004: Scipion: v2.0 (2019-04-23) Diocletian > 00005: currentDir: > /home/user/Data/ScipionUserData/projects/Colette__03_06__20 > 00006: workingDir: Runs/000317_SphireProtCRYOLOTraining > 00007: runMode: Restart > 00008: MPI: 1 > 00009: threads: 1 > 00010: Starting at step: 1 > 00011: Running steps > 00012: STARTED: convertInputStep, step 1 > 00013: 2020-06-04 14:19:55.349748 > 00014: FINISHED: convertInputStep, step 1 > 00015: 2020-06-04 14:19:55.477612 > 00016: STARTED: createConfigStep, step 2 > 00017: 2020-06-04 14:19:55.480179 > 00018: FINISHED: createConfigStep, step 2 > 00019: 2020-06-04 14:19:55.481720 > 00020: STARTED: cryoloModelingStep, step 3 > 00021: 2020-06-04 14:19:55.483884 > 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on > conda being in the PATH > 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w > 5 -g 0 -e 10 --fine_tune > 00024: /bin/sh: conda: command not found > 00025: Traceback (most recent call last): > 00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 186, in run > 00027: self._run() > 00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 237, in _run > 00029: resultFiles = self._runFunc() > 00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 233, in _runFunc > 00031: return self._func(*self._args) > 00032: File > "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", > line 246, in cryoloModelingStep > 00033: self.runCryoloTrain(5, extraArgs=extraArgs) > 00034: File > "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", > line 243, in runCryoloTrain > 00035: cwd=self._getWorkDir()) > 00036: File > "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", > line 220, in runCryolo > 00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), > cwd=cwd) > 00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line > 1311, in runJob > 00039: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > 00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", line > 70, in runJob > 00041: env=env, cwd=cwd, gpuList=self.getGpuList()) > 00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line 52, > in runJob > 00043: return runCommand(command, env, cwd) > 00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line 67, > in runCommand > 00045: env=env, cwd=cwd) > 00046: File "/usr/local/scipion/software/lib/python2.7/subprocess.py", > line 190, in check_call > 00047: raise CalledProcessError(retcode, cmd) > 00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && > cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned > non-zero exit status 127 > 00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && > cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned > non-zero exit status 127 > 00050: FAILED: cryoloModelingStep, step 3 > 00051: 2020-06-04 14:19:55.510445 > 00052: *** Last status is failed > 00053: ------------------- PROTOCOL FAILED (DONE 3/4) > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2020-06-04 12:40:16
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Dear colleagues, I have a problems running shire cryo training protocol in SCIPION. Do you know how to fix it? Thank you! Sincerely, Dmitry ============== RUNSTDOUT =============== UNNING PROTOCOL ----------------- 00002: HostName: dataanalysisserver1 00003: PID: 69964 00004: Scipion: v2.0 (2019-04-23) Diocletian 00005: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20 00006: workingDir: Runs/000317_SphireProtCRYOLOTraining 00007: runMode: Restart 00008: MPI: 1 00009: threads: 1 00010: Starting at step: 1 00011: Running steps 00012: STARTED: convertInputStep, step 1 00013: 2020-06-04 14:19:55.349748 00014: FINISHED: convertInputStep, step 1 00015: 2020-06-04 14:19:55.477612 00016: STARTED: createConfigStep, step 2 00017: 2020-06-04 14:19:55.480179 00018: FINISHED: createConfigStep, step 2 00019: 2020-06-04 14:19:55.481720 00020: STARTED: cryoloModelingStep, step 3 00021: 2020-06-04 14:19:55.483884 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune 00024: /bin/sh: conda: command not found 00025: Traceback (most recent call last): 00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in run 00027: self._run() 00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in _run 00029: resultFiles = self._runFunc() 00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc 00031: return self._func(*self._args) 00032: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 246, in cryoloModelingStep 00033: self.runCryoloTrain(5, extraArgs=extraArgs) 00034: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 243, in runCryoloTrain 00035: cwd=self._getWorkDir()) 00036: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", line 220, in runCryolo 00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd) 00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 1311, in runJob 00039: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", line 70, in runJob 00041: env=env, cwd=cwd, gpuList=self.getGpuList()) 00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line 52, in runJob 00043: return runCommand(command, env, cwd) 00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line 67, in runCommand 00045: env=env, cwd=cwd) 00046: File "/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, in check_call 00047: raise CalledProcessError(retcode, cmd) 00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00050: FAILED: cryoloModelingStep, step 3 00051: 2020-06-04 14:19:55.510445 00052: *** Last status is failed 00053: ------------------- PROTOCOL FAILED (DONE 3/4) ============================================================ ======== RUN LOG ======= RUNNING PROTOCOL ----------------- 00002: HostName: dataanalysisserver1 00003: PID: 69964 00004: Scipion: v2.0 (2019-04-23) Diocletian 00005: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20 00006: workingDir: Runs/000317_SphireProtCRYOLOTraining 00007: runMode: Restart 00008: MPI: 1 00009: threads: 1 00010: Starting at step: 1 00011: Running steps 00012: STARTED: convertInputStep, step 1 00013: 2020-06-04 14:19:55.349748 00014: FINISHED: convertInputStep, step 1 00015: 2020-06-04 14:19:55.477612 00016: STARTED: createConfigStep, step 2 00017: 2020-06-04 14:19:55.480179 00018: FINISHED: createConfigStep, step 2 00019: 2020-06-04 14:19:55.481720 00020: STARTED: cryoloModelingStep, step 3 00021: 2020-06-04 14:19:55.483884 00022: WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH 00023: conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune 00024: /bin/sh: conda: command not found 00025: Traceback (most recent call last): 00026: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in run 00027: self._run() 00028: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in _run 00029: resultFiles = self._runFunc() 00030: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc 00031: return self._func(*self._args) 00032: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 246, in cryoloModelingStep 00033: self.runCryoloTrain(5, extraArgs=extraArgs) 00034: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/protocols/protocol_cryolo_training.py", line 243, in runCryoloTrain 00035: cwd=self._getWorkDir()) 00036: File "/usr/local/scipion/software/lib/python2.7/site-packages/sphire/__init__.py", line 220, in runCryolo 00037: protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd) 00038: File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 1311, in runJob 00039: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00040: File "/usr/local/scipion/pyworkflow/protocol/executor.py", line 70, in runJob 00041: env=env, cwd=cwd, gpuList=self.getGpuList()) 00042: File "/usr/local/scipion/pyworkflow/utils/process.py", line 52, in runJob 00043: return runCommand(command, env, cwd) 00044: File "/usr/local/scipion/pyworkflow/utils/process.py", line 67, in runCommand 00045: env=env, cwd=cwd) 00046: File "/usr/local/scipion/software/lib/python2.7/subprocess.py", line 190, in check_call 00047: raise CalledProcessError(retcode, cmd) 00048: CalledProcessError: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00049: Protocol failed: Command ' conda activate cryolo-1.6.1 && cryolo_train.py -c config.json -w 5 -g 0 -e 10 --fine_tune' returned non-zero exit status 127 00050: FAILED: cryoloModelingStep, step 3 00051: 2020-06-04 14:19:55.510445 00052: *** Last status is failed 00053: ------------------- PROTOCOL FAILED (DONE 3/4) |
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From: 范宏成 <187...@16...> - 2020-06-04 11:57:11
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Ok I got it. Thank you Grigory! | | 范宏成 | | 邮箱：187...@16... | 签名由 网易邮箱大师 定制 On 06/04/2020 18:40, Grigory Sharov wrote: Hi Hongcheng, I've never used this command before, I believe ccpem would be a better place to ask. 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 e-mail: gs...@mr... On Thu, Jun 4, 2020 at 11:35 AM 范宏成 <187...@16...> wrote: Hi all, Does anyone know how to judge the best box size from this picture using relion_plot_delocalization command? Thank you! Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-06-04 10:41:16
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Hi Hongcheng, I've never used this command before, I believe ccpem would be a better place to ask. 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 Thu, Jun 4, 2020 at 11:35 AM 范宏成 <187...@16...> wrote: > Hi all, > Does anyone know how to judge the best box size from this picture using > relion_plot_delocalization command? Thank you! > > > Hongcheng Fan > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D> > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 定制 > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: 范宏成 <187...@16...> - 2020-06-04 10:35:26
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Hi all, Does anyone know how to judge the best box size from this picture using relion_plot_delocalization command? Thank you! Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 |
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From: Grigory S. <sha...@gm...> - 2020-05-28 20:29:37
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Hello Dmitry, looking at the output, GCTF has failed to run. Most often this happens due to incompatibility of the binary you used and cuda / gpu cc version. 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 Thu, May 28, 2020 at 9:22 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > During testing the new hardware/software, we have one more issue – > > The gCTF results in the black frames output for the psdFile column. > > > Could you please suggest the solution? > > > Thank you > > > Sincerely, > > Dmitry > > > > > runstdout > > ……………………… > > All 1 files to be searched and refined: > > 04024: > Runs/003956_ProtGctf/tmp/mic_0024/20170629_00049_frameImage_aligned_mic.mrc > > 04025: Warning in function gctf_open_sumlog(), file src/ctf.cu on line > 2965:No output ctfstar file! You may have to extract CTF information from > *_gctf.log! > > 04026: > >>>>>>TIME<<<<<< > PREPARATION: 0.363971s > > 04027: Reading file: > Runs/003956_ProtGctf/tmp/mic_0024/20170629_00049_frameImage_aligned_mic.mrc > > 04028: > >>>>>>TIME<<<<<< > READING: 0.031053s > > 04029: . > > 04030: >>>>>>TIME<<<<<< > FFT: 1.224681s > > 04031: > > 04032: Defocus_U Defocus_V Angle CCC > > 04033: 2450.00 2550.00 27.18 -nan Final Values > > 04034: > > 04035: >>>>>>TIME<<<<<< > 1S2R: 0.003816s > > 04036: Resolution limit estimated by EPA: 1.916 > > 04037: Estimated Bfactor: -0.00 > > 04038: > >>>>>>TIME<<<<<< LOCAL > REFINE: 0.000000s > > 04039: > >>>>>>TIME<<<<<< PHASE > FLIP: 0.000000s > > 04040: Processing done successfully. > > 04041: > ------------------------------------------------------------------------------------------------------------------------------- > > 04042: > > 04043: FINISHED: estimateCtfStep, step 24 > > 04044: 2020-05-28 22:13:10.064454 > > 04045: STARTED: createOutputStep, step 25 > > 04046: 2020-05-28 22:13:10.094255 > > 04047: FINISHED: createOutputStep, step 25 > > 04048: 2020-05-28 22:13:10.095781 > > 04049: *** Last status is finished > > 04050: Cleaning temp folder.... > > 04051: ------------------- PROTOCOL FINISHED > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry A. S. <sem...@gm...> - 2020-05-28 20:22:03
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Dear colleagues,
During testing the new hardware/software, we have one more issue –
The gCTF results in the black frames output for the psdFile column.
Could you please suggest the solution?
Thank you
Sincerely,
Dmitry
runstdout
………………………
All 1 files to be searched and refined:
04024:
Runs/003956_ProtGctf/tmp/mic_0024/20170629_00049_frameImage_aligned_mic.mrc
04025: Warning in function gctf_open_sumlog(), file src/ctf.cu on line
2965:No output ctfstar file! You may have to extract CTF information
from *_gctf.log!
04026: >>>>>>TIME<<<<<<
PREPARATION: 0.363971s
04027: Reading file:
Runs/003956_ProtGctf/tmp/mic_0024/20170629_00049_frameImage_aligned_mic.mrc
04028: >>>>>>TIME<<<<<<
READING: 0.031053s
04029: .
04030: >>>>>>TIME<<<<<<
FFT: 1.224681s
04031:
04032: Defocus_U Defocus_V Angle CCC
04033: 2450.00 2550.00 27.18 -nan Final Values
04034:
04035: >>>>>>TIME<<<<<<
1S2R: 0.003816s
04036: Resolution limit estimated by EPA: 1.916
04037: Estimated Bfactor: -0.00
04038: >>>>>>TIME<<<<<<
LOCAL REFINE: 0.000000s
04039: >>>>>>TIME<<<<<<
PHASE FLIP: 0.000000s
04040: Processing done successfully.
04041:
-------------------------------------------------------------------------------------------------------------------------------
04042:
04043: FINISHED: estimateCtfStep, step 24
04044: 2020-05-28 22:13:10.064454
04045: STARTED: createOutputStep, step 25
04046: 2020-05-28 22:13:10.094255
04047: FINISHED: createOutputStep, step 25
04048: 2020-05-28 22:13:10.095781
04049: *** Last status is finished
04050: Cleaning temp folder....
04051: ------------------- PROTOCOL FINISHED
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From: Pablo C. <pc...@cn...> - 2020-05-27 15:24:39
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Dear Dmitry....this happens when none of the movies worked. Usually is related to the configuration which is a combination of matching: 1.- The binary file used (specified in the config.file), 2.- The cuda version used 3.- In some cases the GPU architecture also affects the success This apply to all software that is distributed as binaries. Check the plugin page, https://github.com/scipion-em/scipion-em-motioncorr You need to play with MOTIONCOR2_CUDA_LIB, and MOTIONCOR2 variables. Example: (I've got motioncor2 1.2.1) 1.- ls -l <scipion__home>/software/em/motioncor2-1.2.1/bin/ MotionCor2_1.2.1-Cuda80 MotionCor2_1.2.1-Cuda91 MotionCor2_1.2.1-Cuda92 Set MOTIONCOR2 to the one matching your CUDA version installed 2.- If CUDA_LIB at scipion.conf does not match you'll need to set MOTIONCOR2_CUDA_LIB to match the chosen binary. In this case, the GPU architecture does not affect. scipion printenv | grep MOTIONCOR2 will help you to check those values. On 27/5/20 16:12, Dmitry A. Semchonok wrote: > Dear colleagues, > > During the test of SCIPION on the new server we got the error on > during motion correction step (original files are in the attachment) > > How to fix this issue? > > Thank you! > > Sincerely, > Dmitry > > > > > > > ========================================= > run > > 2020-05-27 15:47:19,297 INFO: [35mSTARTED[0m: waitForThreadStep, > step 12 > 2020-05-27 15:47:19,297 INFO: 2020-05-27 15:47:19.297160 > 2020-05-27 15:47:19,301 INFO: [35mFINISHED[0m: waitForThreadStep, > step 12 > 2020-05-27 15:47:19,301 INFO: 2020-05-27 15:47:19.299252 > 2020-05-27 15:47:19,302 INFO: [35mSTARTED[0m: createOutputStep, step 13 > 2020-05-27 15:47:19,302 INFO: 2020-05-27 15:47:19.302209 > 2020-05-27 15:47:19,305 ERROR: [31mProtocol failed: [31mAll movies > failed, didn't create outputMicrographs.Please review movie processing > steps above.[0m[0m > 2020-05-27 15:47:19,308 INFO: [35mFAILED[0m: createOutputStep, step 13 > 2020-05-27 15:47:19,308 INFO: 2020-05-27 15:47:19.304107 > 2020-05-27 15:47:19,311 INFO: [32m------------------- PROTOCOL > FAILED (DONE 13/13)[0m > 2020-05-27 15:47:19,321 INFO: [32m------------------- PROTOCOL > FAILED (DONE 13/13)[0m > > > > ========================================== > run.stdout > > > ...... Frame ( 25) shift: 0.000 0.000 > ...... Frame ( 26) shift: 0.000 0.000 > ...... Frame ( 27) shift: 0.000 0.000 > ...... Frame ( 28) shift: 0.000 0.000 > ...... Frame ( 29) shift: 0.000 0.000 > ...... Frame ( 30) shift: 0.000 0.000 > > ERROR: Movie failed > > [35mFINISHED[0m: processMovieStep, step 11 > 2020-05-27 15:47:19.274026 > [33mWARNING: Movie > Runs/000002_ProtImportMovies/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions.mrc > has empty alignment data, can't add it to output set.[0m > [33mWARNING: Micrograph > Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic.mrc > was not generated, can't add it to output set.[0m > [33mWARNING: Micrograph > Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic_DW.mrc > was not generated, can't add it to output set.[0m > [35mSTARTED[0m: waitForThreadStep, step 12 > 2020-05-27 15:47:19.297160 > [35mFINISHED[0m: waitForThreadStep, step 12 > 2020-05-27 15:47:19.299252 > [35mSTARTED[0m: createOutputStep, step 13 > 2020-05-27 15:47:19.302209 > Traceback (most recent call last): > File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, > in run > self._run() > File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, > in _run > resultFiles = self._runFunc() > File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, > in _runFunc > return self._func(*self._args) > File > "/usr/local/scipion/pyworkflow/em/protocol/protocol_align_movies.py", > line 117, in createOutputStep > raise Exception(redStr("All movies failed, didn't create > outputMicrographs." > Exception: [31mAll movies failed, didn't create > outputMicrographs.Please review movie processing steps above.[0m > [31mProtocol failed: [31mAll movies failed, didn't create > outputMicrographs.Please review movie processing steps above.[0m[0m > [35mFAILED[0m: createOutputStep, step 13 > 2020-05-27 15:47:19.304107 > [32m------------------- PROTOCOL FAILED (DONE 13/13)[0m > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry A. S. <sem...@gm...> - 2020-05-27 14:13:03
|
Dear colleagues,
During the test of SCIPION on the new server we got the error on during
motion correction step (original files are in the attachment)
How to fix this issue?
Thank you!
Sincerely,
Dmitry
=========================================
run
2020-05-27 15:47:19,297 INFO: [35mSTARTED[0m: waitForThreadStep, step
12
2020-05-27 15:47:19,297 INFO: 2020-05-27 15:47:19.297160
2020-05-27 15:47:19,301 INFO: [35mFINISHED[0m: waitForThreadStep,
step 12
2020-05-27 15:47:19,301 INFO: 2020-05-27 15:47:19.299252
2020-05-27 15:47:19,302 INFO: [35mSTARTED[0m: createOutputStep, step
13
2020-05-27 15:47:19,302 INFO: 2020-05-27 15:47:19.302209
2020-05-27 15:47:19,305 ERROR: [31mProtocol failed: [31mAll movies
failed, didn't create outputMicrographs.Please review movie processing
steps above.[0m[0m
2020-05-27 15:47:19,308 INFO: [35mFAILED[0m: createOutputStep, step
13
2020-05-27 15:47:19,308 INFO: 2020-05-27 15:47:19.304107
2020-05-27 15:47:19,311 INFO: [32m------------------- PROTOCOL FAILED
(DONE 13/13)[0m
2020-05-27 15:47:19,321 INFO: [32m------------------- PROTOCOL FAILED
(DONE 13/13)[0m
==========================================
run.stdout
...... Frame ( 25) shift: 0.000 0.000
...... Frame ( 26) shift: 0.000 0.000
...... Frame ( 27) shift: 0.000 0.000
...... Frame ( 28) shift: 0.000 0.000
...... Frame ( 29) shift: 0.000 0.000
...... Frame ( 30) shift: 0.000 0.000
ERROR: Movie failed
[35mFINISHED[0m: processMovieStep, step 11
2020-05-27 15:47:19.274026
[33mWARNING: Movie
Runs/000002_ProtImportMovies/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions.mrc
has empty alignment data, can't add it to output set.[0m
[33mWARNING: Micrograph
Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic.mrc
was not generated, can't add it to output set.[0m
[33mWARNING: Micrograph
Runs/000085_ProtMotionCorr/extra/FoilHole_22185017_Data_22186404_22186405_20190522_2012_Fractions_aligned_mic_DW.mrc
was not generated, can't add it to output set.[0m
[35mSTARTED[0m: waitForThreadStep, step 12
2020-05-27 15:47:19.297160
[35mFINISHED[0m: waitForThreadStep, step 12
2020-05-27 15:47:19.299252
[35mSTARTED[0m: createOutputStep, step 13
2020-05-27 15:47:19.302209
Traceback (most recent call last):
File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 186, in
run
self._run()
File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 237, in
_run
resultFiles = self._runFunc()
File "/usr/local/scipion/pyworkflow/protocol/protocol.py", line 233, in
_runFunc
return self._func(*self._args)
File
"/usr/local/scipion/pyworkflow/em/protocol/protocol_align_movies.py",
line 117, in createOutputStep
raise Exception(redStr("All movies failed, didn't create
outputMicrographs."
Exception: [31mAll movies failed, didn't create
outputMicrographs.Please review movie processing steps above.[0m
[31mProtocol failed: [31mAll movies failed, didn't create
outputMicrographs.Please review movie processing steps above.[0m[0m
[35mFAILED[0m: createOutputStep, step 13
2020-05-27 15:47:19.304107
[32m------------------- PROTOCOL FAILED (DONE 13/13)[0m |
|
From: Juha H. <juh...@he...> - 2020-05-26 12:21:44
|
Hi David, I propose to create a new protocol for refinement, then select the option to continue from a previous refinement (you should see the interrupted refinement as an input). Then in the additional parameters field (the last tab) add option --force_converge. Then the continuation refinement will enter the last final iteration straight away. If you would rather import the particles using a STAR file and calculate the half maps separately, you should check that the particle orientations and origins, in addition to the half data set assignment, have been imported properly. I am not sure if this happens currently, but you can check by examining the particle set (display results) and changing to the list view. Best wishes, Juha On Mon, May 25, 2020 at 10:43 AM DAVID GIL CANTERO <dg...@cn...> wrote: > > Hello, I had an auto-refine running whose resolution have changed just > 0.01A from the previous iteration to the last one (not the final). As > the difference is not great and the iterations takes more than 2 days > I stopped it but now, none of the protocols admit it as an input, it > did not even appear in the inputs list. I have tried to import the > .star file with the angles from the last iteration but when > reconstructed, the resolution is far worst than what said in the > refinement. I guess the problem is having aborted the refinement, is > it any way to by-pass this issue? > > Thank you. > David. > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: DAVID G. C. <dg...@cn...> - 2020-05-25 07:33:25
|
Hello, I had an auto-refine running whose resolution have changed just 0.01A from the previous iteration to the last one (not the final). As the difference is not great and the iterations takes more than 2 days I stopped it but now, none of the protocols admit it as an input, it did not even appear in the inputs list. I have tried to import the .star file with the angles from the last iteration but when reconstructed, the resolution is far worst than what said in the refinement. I guess the problem is having aborted the refinement, is it any way to by-pass this issue? Thank you. David. |
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From: Marta M. <mm...@cn...> - 2020-05-20 10:01:48
|
Hi Dmitry, good suggestion but we do not have that tool yet. Best regards, MARTA Quoting Carlos Oscar Sorzano <co...@cn...>: > Dear Dmitry, > > I am not aware of such a tool, Marta may know better than myself, > but I agree that it is a good suggestion if it is not already there. > > Kind regards, Carlos Oscar > > El 19/05/2020 a las 16:48, Dmitry A. Semchonok escribió: >> >> Dear colleagues, >> >> I want to compare 2 models that have some differences: the same >> subunits but repositioned, missing structures, etc. >> >> Is there a tool in SCIPION that can: >> >> - Make a list of structure A (all components/residues). A list of >> elements in Structure B. >> >> - Compare and report the missing parts in structure B compared to >> structure A? Maybe also the differences in distances between the >> same helices in structure B compared to structure A? >> >> Thank you! >> >> Sincerely, >> >> Dmitry >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mm...@cn... |
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