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[scipion-users] Issues with Gautomatch
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From: Maria D. M. P. R. <mar...@cp...> - 2020-06-16 09:14:44
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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
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