创建 Conda 环境失败状态：143

Question

I am trying to run a nexflow pipeline on some data via the Linux command line, but when I do so, it fails because it fails to create the Conda environment.

It looks like it tries to run the pipeline anyway, despite the environment not being set up properly, and so generates an error message. Any help would be much appreciated. Here is the error message:

Error executing process > 'my_process (1)'
Caused by:
  Failed to create Conda environment
  command: conda env create --prefix /my_file_path-6bf38a923b48a255f96ea3d66d372e6c --file /my_file_path/environment.yml
  status : 143
  message:

Here is my environment.yml file:

name: pipeline_name
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - filtlong
  - blast==2.5
  - minimap2 
  - samtools 
  - pysam 
  - pandas 
  - matplotlib 
  - pysamstats
  - seaborn 
  - medaka
  - bedtools
  - bedops
  - seqtk
  - bioawk
  - sniffles

Answer 1

Not an answer to this question, but if you get a similar failure with a different exit status (120, not 143), try the fix in this thread. Reposting it here:

conda environment from file not working using nextflow · Issue #1081 · nextflow-io/nextflow: https://github.com/nextflow-io/nextflow/issues/1081

pditommaso commented on Mar 18, 2019
The 120 exit status signals that it was reached the creation timeout. Try increasing it, eg.

conda.createTimeout = '1 h'