Snakemake包装器突然停止工作

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英文:

Snakemake wrappers suddenly stopped working

问题

有一个突然出现的无法避免的Python版本冲突问题，该如何解决？

解决这个问题的方法是确保Snakefile中的规则（rule）在执行时使用与Snakefile中定义的Conda环境相匹配的Python版本。根据你的错误信息，Snakefile正在尝试使用Python版本低于3.7的环境，但Snakefile中定义的Conda环境可能要求使用Python版本3.7或更高版本。

要解决这个问题，你可以采取以下步骤：

  1. 更新Conda环境： 确保你的Conda环境中包含Python版本3.7或更高版本。你可以通过运行以下命令来更新Conda环境：

    conda install python=3.7

    如果已经存在一个包含所需Python版本的环境，则可以跳过这一步。

  2. 修改Snakefile规则： 在Snakefile中的每个规则（rule）的conda部分中，指定要使用的Conda环境的名称。例如：

    conda: "your_environment_name"

    请确保your_environment_name与你的Conda环境的名称匹配。

  3. 重新运行Snakefile： 更新后的Snakefile应该能够使用正确的Python环境来执行规则。

通过执行上述步骤，你应该能够解决Python版本冲突的问题，使你的Snakefile能够正常运行。如果仍然遇到问题，请确保你的Conda环境中包含所需的Python包和依赖项，并检查Snakefile中的其他配置是否正确。

英文:

I have this wrappers in my snakemake file

rule fastqc:
    input:
        "reads/{sample}_trimmed.fq.gz"
    output:
        html="qc/fastqc/{sample}.html",
        zip="qc/fastqc/{sample}_fastqc.zip" # the suffix _fastqc.zip is necessary for multiqc to find the file
    params:
        extra = "--quiet"
    log:
        "logs/fastqc/{sample}.log"
    threads: config["resources"]["fastqc"]["cpu"]
    conda:
        "envs/qc.yaml"
    wrapper:
        "v1.31.1/bio/fastqc"

qc.yaml:

name: qc
channels: 
  - bioconda
dependencies:
  - python
  - fastqc
  - multiqc

This normally works, but suddenly it stopped working (I have not changed the code) and I get this error:

[Thu Jun  8 15:34:53 2023]
rule fastqc:
    input: reads/S15_trimmed.fq.gz
    output: qc/fastqc/S15.html, qc/fastqc/S15_fastqc.zip
    log: logs/fastqc/S15.log
    jobid: 2
    reason: Missing output files: qc/fastqc/S15_fastqc.zip
    wildcards: sample=S15
    threads: 4
    resources: tmpdir=/tmp

[Thu Jun  8 15:34:53 2023]
rule fastqc:
    input: reads/L8_trimmed.fq.gz
    output: qc/fastqc/L8.html, qc/fastqc/L8_fastqc.zip
    log: logs/fastqc/L8.log
    jobid: 6
    reason: Missing output files: qc/fastqc/L8_fastqc.zip
    wildcards: sample=L8
    threads: 4
    resources: tmpdir=/tmp

[Thu Jun  8 15:34:53 2023]
rule fastqc:
    input: reads/S8_trimmed.fq.gz
    output: qc/fastqc/S8.html, qc/fastqc/S8_fastqc.zip
    log: logs/fastqc/S8.log
    jobid: 4
    reason: Missing output files: qc/fastqc/S8_fastqc.zip
    wildcards: sample=S8
    threads: 4
    resources: tmpdir=/tmp

python -c "from __future__ import print_function; import sys, json; print(json.dumps([sys.version_info.major, sys.version_info.minor]))"
Activating conda environment: .snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_
python -c "from __future__ import print_function; import sys, json; print(json.dumps([sys.version_info.major, sys.version_info.minor]))"
Activating conda environment: .snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_
python -c "from __future__ import print_function; import sys, json; print(json.dumps([sys.version_info.major, sys.version_info.minor]))"
Activating conda environment: .snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_
Environment defines Python version < 3.7. Using Python of the main process to execute script. Note that this cannot be avoided, because the script uses data structures from Snakemake which are Python >=3.7 only.
Environment defines Python version < 3.7. Using Python of the main process to execute script. Note that this cannot be avoided, because the script uses data structures from Snakemake which are Python >=3.7 only.
/home/user/mambaforge/envs/snakemake/bin/python3.11 /mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/scripts/tmpx1titff7.wrapper.py
/home/user/mambaforge/envs/snakemake/bin/python3.11 /mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/scripts/tmpw1yrfmqi.wrapper.py
Activating conda environment: .snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_
Activating conda environment: .snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_
Environment defines Python version < 3.7. Using Python of the main process to execute script. Note that this cannot be avoided, because the script uses data structures from Snakemake which are Python >=3.7 only.
/home/user/mambaforge/envs/snakemake/bin/python3.11 /mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/scripts/tmpnh80ovk0.wrapper.py
Activating conda environment: .snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_
Traceback (most recent call last):
  File "/mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/scripts/tmpx1titff7.wrapper.py", line 17, in <module>
    from snakemake_wrapper_utils.snakemake import get_mem
ModuleNotFoundError: No module named 'snakemake_wrapper_utils'
Traceback (most recent call last):
  File "/mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/scripts/tmpw1yrfmqi.wrapper.py", line 17, in <module>
    from snakemake_wrapper_utils.snakemake import get_mem
ModuleNotFoundError: No module named 'snakemake_wrapper_utils'
Traceback (most recent call last):
  File "/mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/scripts/tmpnh80ovk0.wrapper.py", line 17, in <module>
    from snakemake_wrapper_utils.snakemake import get_mem
ModuleNotFoundError: No module named 'snakemake_wrapper_utils'
[Thu Jun  8 15:34:54 2023]
Error in rule fastqc:
    jobid: 4
    input: reads/S8_trimmed.fq.gz
    output: qc/fastqc/S8.html, qc/fastqc/S8_fastqc.zip
    log: logs/fastqc/S8.log (check log file(s) for error details)
    conda-env: /mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_

[Thu Jun  8 15:34:54 2023]
Error in rule fastqc:
    jobid: 2
    input: reads/S15_trimmed.fq.gz
    output: qc/fastqc/S15.html, qc/fastqc/S15_fastqc.zip
    log: logs/fastqc/S15.log (check log file(s) for error details)
    conda-env: /mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_

[Thu Jun  8 15:34:54 2023]
Error in rule fastqc:
    jobid: 6
    input: reads/L8_trimmed.fq.gz
    output: qc/fastqc/L8.html, qc/fastqc/L8_fastqc.zip
    log: logs/fastqc/L8.log (check log file(s) for error details)
    conda-env: /mnt/4TB_SSD/analyses/CRISPR/test/.snakemake/conda/32ae7e363cfd65f035e232e794d5bc2b_

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

There seems to be a Python version conflict suddenly that cannot be avoided. How can I solve this?

答案1

得分: 1

我不知道它如何可能之前能工作，现在在没有任何更改的情况下不工作。您使用的Snakemake版本是多少？Snakemake的调用是什么？您是否在conda环境中运行Snakemake？

此外，当您使用包装器时，包装器定义了自己的环境，因此您不应该在使用包装器的规则中定义conda。请删除它，使其看起来像这样：

rule fastqc:
    input:
        "reads/{sample}_trimmed.fq.gz"
    output:
        html="qc/fastqc/{sample}.html",
        zip="qc/fastqc/{sample}_fastqc.zip"  # 必须使用后缀_fastqc.zip以便multiqc找到文件
    params:
        extra="--quiet"
    log:
        "logs/fastqc/{sample}.log"
    threads: config["resources"]["fastqc"]["cpu"]
    wrapper:
        "v1.31.1/bio/fastqc"

Snakemake现在将使用包装器conda环境而不是规则环境来运行包装器代码，从而解决了问题。

英文:

I have no idea how it is possible that it worked before and now it does not work without any changes whatsoever. What snakemake version do you use? What was the snakemake call? Do you run snakemake inside conda environment?

Further, when you use a wrapper, wrapper defines its own environment, therefore you should not define conda in rules using wrapper. Remove it so it would look like this:

rule fastqc:
    input:
        "reads/{sample}_trimmed.fq.gz"
    output:
        html="qc/fastqc/{sample}.html",
        zip="qc/fastqc/{sample}_fastqc.zip" # the suffix _fastqc.zip is necessary for multiqc to find the file
    params:
        extra = "--quiet"
    log:
        "logs/fastqc/{sample}.log"
    threads: config["resources"]["fastqc"]["cpu"]
    wrapper:
        "v1.31.1/bio/fastqc"

Snakemake will now use the wrapper conda environment instead of the rule environment to run the wrapper code, solving the problem.

huangapple
  • 本文由 发表于 2023年6月8日 22:49:31
  • 转载请务必保留本文链接：https://go.coder-hub.com/76433097.html
  • python
  • snakemake
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