[scipion-users] shire cryo training protocol failed from running

[Dmitry S. <Sem...@gm...>]

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)