[scipion-users] error during test sphire

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

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

>>> ERROR running protocol sphire - janni denoising
    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
-------------------------------

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