Question

我是snakemake的新手，并且是第一次使用奇点。我已经在计算机上本地下载了Singularity和docker。我试图运行我的snakemake脚本，但是出现错误。

RuleException：第40行的CalledProcessError /home/fr2424/sib/gniang/Documents/Roscoff/scripts/snakemake_container_test/container_test.py：命令'set -euo pipefail;奇异执行 /home/fr2424/sib/gniang/Documents/Roscoff/scripts/snakemake_container_test/.snakemake/singularity/baf906ce094e5594a017121e6b20ed12.simg bash -c“ /home/fr2424/sib/gniang/Documents/Roscoff/scripts/snakemake_container_test/input/SRR1300319_2.fastq.gz --outdir /home/fr2424/sib/gniang/Documents/Roscoff/scripts/snakemake_container_test/output/fastqc_raw/SRR1300319_2.fastqc.zip --threads 1＆> “”返回非零退出状态255。

文件“ /home/fr2424/sib/gniang/Documents/Roscoff/scripts/snakemake_container_test/container_test.py”，第40行，位于__rule_raw_fastqc 运行中的文件“ /usr/lib/python3.6/concurrent/futures/thread.py”，第56行在完成当前正在运行的作业后将退出。

snakemake脚本似乎找不到奇点图像。但是当我查看.snakemake文件夹中的图像时，它存在。所以我不知道如何解决它。你能帮我吗？这是我的脚本：

#!/usr/bin/python

# Imports
import os

# Get current working directory
dir_path = os.getcwd()

# User defined ouput directory
OUT_DIR = config["directories"]["outdir"]

# User defined ouput directory
INPUT_DIR = config["directories"]["indir"]

# Relative output directories
FASTQC_RAW_DIR = OUT_DIR + "fastqc_raw/"


SLES = glob_wildcards(INPUT_DIR + "{smp}.fastq.gz")
print(SLES)
NB_SLES = len(SLES)

# ALL
rule all:
    input:
        fastqc_raw_out = expand(FASTQC_RAW_DIR + "{smp}.fastqc.zip", smp=SLES.smp),

# FASTQC: This rule is use to generate an evaluation report raw FASTQ files
# provided by the user.
rule raw_fastqc:
    input:
        fastq = INPUT_DIR + "{smp}.fastq.gz"
    output:
        fastqc_raw_out = FASTQC_RAW_DIR+"{smp}.fastqc.zip",
    singularity:
        "docker://biocontainers/fastqc"
    output:
        OUT_DIR + "logs/fastqc/raw_fastqc.log"
    shell:
        """
        {input.fastq} --outdir {output.fastqc_raw_out} --threads {threads} &> {log}


"""

谢谢！

在snakemake中使用奇异选项

0 个答案: