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PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
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Problem of Python version on cluster #681

Closed Lcornet closed 5 years ago

Lcornet commented 5 years ago

I have a problem with Python version after conda install. I run fc_run.py on local and it works.

#install conda python 3.6
conda create -n denovo_asm
source activate denovo_asm
conda install -c bioconda pb-assembly

#run with this error
Job 968507 exited with exit code 127.
[ERROR]Task Node(0-rawreads/build) failed with exit-code=127
[ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
[ERROR]ready: set([])
    submitted: set([])

export PATH=$PATH:/bin
+ export PATH=/media/vol2/home/lcornet/miniconda3/bin:/media/vol1/apps/pyenv/shims:/media/vol1/apps/pyenv/bin:/media/vol1/apps/perlbrew/bin:/media/vol1/apps/perlbrew/perls/perl-5.22.0-thread-multi/bin:/media/vol1/gridengine/bin/linux-x64:/tmp/968507.1.smallnodes.q:/media/vol2/home/lcornet/miniconda3/envs/denovo_asm/bin:/media/vol2/home/lcornet/miniconda3/bin:/media/vol1/apps/pyenv/shims:/media/vol1/apps/pyenv/bin:/usr/lib64/openmpi/bin:/media/vol1/gridengine/bin/linux-x64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/opt/ibutils/bin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/bin
+ PATH=/media/vol2/home/lcornet/miniconda3/bin:/media/vol1/apps/pyenv/shims:/media/vol1/apps/pyenv/bin:/media/vol1/apps/perlbrew/bin:/media/vol1/apps/perlbrew/perls/perl-5.22.0-thread-multi/bin:/media/vol1/gridengine/bin/linux-x64:/tmp/968507.1.smallnodes.q:/media/vol2/home/lcornet/miniconda3/envs/denovo_asm/bin:/media/vol2/home/lcornet/miniconda3/bin:/media/vol1/apps/pyenv/shims:/media/vol1/apps/pyenv/bin:/usr/lib64/openmpi/bin:/media/vol1/gridengine/bin/linux-x64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/opt/ibutils/bin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/bin
cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build
+ cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build
/bin/bash task.sh
+ /bin/bash task.sh
pyenv: python2.7: command not found

The `python2.7' command exists in these Python versions: 2.7.6 2.7.9

My version of python is 2.7.15. I tried to make an alias, pyenv local to 2.7.6 (then i have the error no module named pypeflow) Can you help me ?

Luc,