Snakemake Conda 环境似乎没有激活，尽管它说它是

问题描述

我正在使用 --use-conda 选项运行 Snakemake。 Snakemake 成功创建了环境，其中应该包括 pysam。我能够手动激活这个创建的环境，并在其中运行我的脚本 split_strands.py，它导入模块 pysam，没有任何问题。但是，在运行 Snakemake 管道时，我收到以下错误日志：

Activating conda environment: /projects/ps-yeolab3/ekofman/sc_STAMP_pipeline/STAMP/workflow/.snakemake/conda/7c375b6b
/projects/ps-yeolab3/ekofman/sc_STAMP_pipeline/STAMP/workflow/scripts/split_strands.py:166: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if args.output_fwd_bam is not '-':
/projects/ps-yeolab3/ekofman/sc_STAMP_pipeline/STAMP/workflow/scripts/split_strands.py:171: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if args.output_rev_bam is not '-':
Traceback (most recent call last):
  File "/projects/ps-yeolab3/ekofman/sc_STAMP_pipeline/STAMP/workflow/scripts/split_strands.py",line 20,in <module>
    import pysam
ModuleNotFoundError: No module named 'pysam'
[Mon Mar 29 16:41:06 2021]
Error in rule split_strands:
    jobid: 0
    output: 1_split_strands/TWA1_possorted_genome_bam_MD-GTCGCGACACGAGGTA-1.bam.fwd.bam,1_split_strands/TWA1_possorted_genome_bam_MD-GTCGCGACACGAGGTA-1.bam.rev.bam
    conda-env: /projects/ps-yeolab3/ekofman/sc_STAMP_pipeline/STAMP/workflow/.snakemake/conda/7c375b6b
    shell:
        
        python scripts/split_strands.py -i /projects/ps-yeolab3/ekofman/sc_STAMP_pipeline/STAMP/workflow/inputs/TWA1_possorted_genome_bam_MD-GTCGCGACACGAGGTA-1.bam -f 1_split_strands/TWA1_possorted_genome_bam_MD-GTCGCGACACGAGGTA-1.bam.fwd.bam -r 1_split_strands/TWA1_possorted_genome_bam_MD-GTCGCGACACGAGGTA-1.bam.rev.bam
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down,this might take some time.
Exiting because a job execution Failed. Look above for error message
Nodes:        tscc-1-37

如你所见，虽然它说它是“激活 conda 环境”，但这似乎不是真的，因为随后找不到模块“pysam”，我已经验证在手动激活时会找到它。

这是指定规则的方式：

rule split_strands:
    input: 
        input_bam=config["samples_path"]+"{sample}",index=config["samples_path"]+"{sample}.bai"
    output: 
        output_fwd="1_split_strands/{sample}.fwd.bam",output_rev="1_split_strands/{sample}.rev.bam"
    conda:
        "envs/python2.7.yaml"
    shell:
        """
        python scripts/split_strands.py -i {input.input_bam} -f {output.output_fwd} -r {output.output_rev}
        """

我已验证散列 7c375b6b 对应于 python2.7.yaml 中指定的适当 env。

任何想法可能会发生什么？我的规则正在运行一个集群并通过 qsub 命令提交。

解决方法

事实证明，snakemake 6.0.0+ 的新版本肯定有一些问题。我改用了snakemake 5.8.2，一切正常。不确定到底发生了什么，但似乎与此问题相同：https://github.com/snakemake/snakemake/issues/883