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

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

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)
>
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