Fastq.gz 文件的奇点命令识别问题

Question

我正在使用 Snakemake 和 Singularity 开发霰弹枪宏基因组学管道，但在尝试在 Snakemake 中执行 Singularity 命令来分析 fastq.gz 文件时遇到困难。然后我决定仅运行 Singularity 命令来了解错误，问题是文件无法识别。我的 Snakefile 位于另一个目录中，当我将数据复制到该目录时，管道工作了。我不明白为什么 Singularity 命令在数据的原始目录中不起作用。

singularity exec -B /mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/results/fastqc:/output docker://staphb/fastqc fastqc -o /output /mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/Undetermined_S0_L001_R1_001.fastq.gz /mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/Undetermined_S0_L001_R2_001.fastq.gz


Using cached SIF image
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LANG = "pt_BR.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Skipping '/mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/Undetermined_S0_L001_R1_001.fastq.gz' which didn't exist, or couldn't be read
Skipping '/mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/Undetermined_S0_L001_R2_001.fastq.gz' which didn't exist, or couldn't be read

permissions:
drwxr-xr-x 2 catg catg    0 abr  1 12:26 results
-r-xr-xr-x 1 catg catg 608M jan 13 16:06 Undetermined_S0_L001_R1_001.fastq.gz
-r-xr-xr-x 1 catg catg 606M jan 13 16:08 Undetermined_S0_L001_R2_001.fastq.gz

Answer 1

为了解决问题，我会尝试：

• 检查安装目录，确保包含 fastq.gz 文件的目录包含在列表中：

  回显$SINGULARITY_BINDPATH

• 检查文件路径以确保您的 fastq.gz 位于此处：

  ls /mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/

• 阅读您的 fastq.gz 之一以确保可访问性：

  cat /mnt/share/Equipamentos_NTO/Med_Pers/Illumina_NextSeq/Corridas/run142/BIOINFO/METAGEN/Undependent_S0_L001_R1_001.fastq.gz > /dev/null