Re: [scipion-users] error during test sphire

[Anne-Pascale J. <ann...@i2...>]

Hi Pablo, 

Thanks a lot, it's working now. 

Anne-Pascale 

---------------------------------------------------------------------- 
Anne-Pascale Jaudier 
SICS – I2BC 
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 
01 69 82 34 74 


De: "Pablo Conesa" <pc...@cn...> 
À: "scipion-users" <sci...@li...> 
Envoyé: Lundi 30 Novembre 2020 17:21:34 
Objet: Re: [scipion-users] error during test sphire 



Hi Anne. 

Try setting the CONDA_ACTIVATION_CMD variable like: 


CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh 

Mind the dot (.). 

If that doesn't work try: 

CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh 

On 30/11/20 17:00, Anne-Pascale JAUDIER wrote: 



Hi,

I try the following test with the following  error on the command "conda activate"
The command "conda activate" is working in a interactive shell. 

Thanks,
Anne-Pascale

 scipion tests sphire.tests.test_protocol_janni 

BQ_BEGIN

BQ_BEGIN

BQ_BEGIN

ERROR running protocol sphire - janni denoising 



BQ_END

BQ_END

FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.

*************** LAST 50 LINES OF THE LOG *********************

      threads: 1
 Starting at step: 1
 Running steps
STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise     .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann     iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni     _20190703.h5

CommandNotFoundError: Your shell has not been properly configured to use 'conda      activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
-------------------------------

----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74


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BQ_END

-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 


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