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Re: [scipion-users] Issues with Gautomatch
|
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
>
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