Snakemake 抱怨它找不到它应该在运行指令中创建的文件

Question

考虑以下简单的 snakefile，它试图在 run 指令中写入文件：

rule all:
    input:
        "test.txt"

rule make_test:
    output:
        filename = "test.txt"
    run:
        with open(output.filename) as f:
            f.write("test")

运行结果如下：

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   all
    1   make_test
    2
rule make_test:
    output: test.txt
Error in job make_test while creating output file test.txt.
RuleException:
FileNotFoundError in line 10 of /tmp/Snakefile:
[Errno 2] No such file or directory: 'test.txt'
  File "/tmp/Snakefile", line 10, in __rule_make_test
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

我对此感到惊讶 FileNotFoundError。显然，我没有找到正确的方法来告诉 snakemake 这是我希望规则 make_test 创建的文件。

我还尝试了以下输出语法的修改：

rule all:
    input:
        "test.txt"

rule make_test:
    output:
        "test.txt"
    run:
        with open(output[0]) as f:
            f.write("test")

还是一样的错误

发生了什么事？

Answer 1

我找到了错误的原因：我只是忘记了以写入模式打开文件：

统治一切：输入： "test.txt"

以下作品：

rule make_test:
    output:
        "test.txt"
    run:
        with open(output[0], "w") as f:
            f.write("test")

Snakemake 抱怨它找不到它应该在运行指令中创建的文件

Snakemake complains it can't find the file it is supposed to create in a run instruction

python

file

snakemake

Snakemake 抱怨它找不到它应该在 运行 指令中创建的文件

Snakemake complains it can't find the file it is supposed to create in a run instruction

python

file

snakemake

Snakemake 抱怨它找不到它应该在运行指令中创建的文件