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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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Hanging on setting up Trinity environment #162

Open matthewabirk opened 3 years ago

matthewabirk commented 3 years ago

I have tried to run:

elvers -t 35 config_05.yaml get_data trimmomatic rcorrector fastqc khmer trinity

and elvers is getting hung up on setting up the Trinity environment. It's been here for >24 hours. I killed it and started again in case it was a one-off bug but it's hung again. Any suggestions?

Running command: bash ./run_elvers.sh
    Found configfile at /automounts/workspace/workspace/mbirk/config_05.yaml
    Added default parameters from rule-specific params files.
    Writing full params to /automounts/workspace/workspace/mbirk/.ep_config_05.yaml
Building DAG of jobs...
Creating conda environment /users/mbirk/apps/elvers/elvers/rules/khmer/environment.yml...
Downloading remote packages.
Environment for ../../../../users/mbirk/apps/elvers/elvers/rules/khmer/environment.yml created (location: .snakemake/conda/aaf9595b)
Creating conda environment /users/mbirk/apps/elvers/elvers/rules/rcorrector/environment.yml...
Downloading remote packages.
Environment for ../../../../users/mbirk/apps/elvers/elvers/rules/rcorrector/environment.yml created (location: .snakemake/conda/d6d94ecd)
Removing incomplete Conda environment /users/mbirk/apps/elvers/elvers/rules/trinity/environment.yml...
Creating conda environment /users/mbirk/apps/elvers/elvers/rules/trinity/environment.yml...
Downloading remote packages.