Windows 10中Ubuntu中的Bash脚本不工作

Question

Ubuntu与Mac上的Linux不同吗？抱歉，如果这是个基本问题.我是新手。我正在尝试运行一个bash脚本，它用一些FASTQ文件创建一个.sh脚本。这可以在Mac操作系统上的终端上使用。我试图在我的Windows笔记本上运行它，它忽略了我对#s的逃避，只说找不到几个命令。我试过使用dos2unix，并与cat -A file.sh进行了反复检查，但这并没有帮助。

我试图运行的代码将所有fastq文件保存在一个文件夹中，并使用它们的文件名为SLURM作业提交创建一个.sh文件(我的学校的计算机集群需要它们，我需要制作100+作业脚本)。因此，Mac版本如下：

for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)
do echo -e \
\#\!/bin/bash \
\\n\#SBATCH --partition=nonpre  \# Partition \(job queue\) \
\\n\#SBATCH --requeue                 \# Return job to the queue if preempted \
\\n\#SBATCH --job-name=samples      \# Assign a short name to your job \
\\n\#SBATCH --nodes=1                 \# Number of nodes you require \
\\n\#SBATCH --ntasks=1                \# Total \# of tasks across all nodes \
\\n\#SBATCH --cpus-per-task=64        \# Cores per task \(\>1 if multithread tasks\) \
\\n\#SBATCH --mem=180000              \# Real memory \(RAM\) required \(MB\) \
\\n\#SBATCH --time=72:00:00           \# Total run time limit \(HH:MM:SS\) \
\\n\#SBATCH --output=slurm.%N.${FILE}.out  \# STDOUT output file \
\\n\#SBATCH --error=slurm.%N.${FILE}.err   \# STDERR output file \(optional\) \
\\n \
\\n\#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION \
\\n \
\\nsacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future submissions \
> ${FILE}.sh; 
done

在Windows上运行此程序时，我得到：

Slurm_Generator.sh: line 13: #!/bin/bash: No such file or directory
Slurm_Generator.sh: line 14: \n#SBATCH: command not found
Slurm_Generator.sh: line 16: \n#SBATCH: command not found
Slurm_Generator.sh: line 18: \n#SBATCH: command not found
Slurm_Generator.sh: line 20: \n#SBATCH: command not found
Slurm_Generator.sh: line 22: \n#SBATCH: command not found
Slurm_Generator.sh: line 24: \n#SBATCH: command not found
Slurm_Generator.sh: line 26: \n#SBATCH: command not found
Slurm_Generator.sh: line 28: \n#SBATCH: command not found
Slurm_Generator.sh: line 30: \n#SBATCH: command not found
Slurm_Generator.sh: line 32: \n#SBATCH: command not found
Slurm_Generator.sh: line 35: \n: command not found
Slurm_Generator.sh: line 36: \n#ADD: command not found
Slurm_Generator.sh: line 39: \n: command not found
Slurm_Generator.sh: line 40: \nsacct: command not found

任何帮助都将不胜感激，并对Windows上的Ubuntu与Mac上的终端之间的区别做了一些解释。我尝试过研究这个问题，但是我一直在寻找没有解释的建议代码，或者这不是我的问题。谢谢!

编辑:我试着运行chmod +x script.sh，我会得到上面的错误。我跑错回音了吗？甚至运行：“对于*fastq中的文件；请回显-e，你好；完成”，Command 'hello' not found说

编辑:运行'bash file.sh‘将产生以下结果：bash file.sh生成以下内容(对于我的目录玩具中的5个.fastq文件)：

Slurm_Generator.sh: line 8: #!/bin/bash: No such file or directory
Slurm_Generator.sh: line 9: \n#SBATCH: command not found
Slurm_Generator.sh: line 11: \n#SBATCH: command not found
Slurm_Generator.sh: line 13: \n#SBATCH: command not found
Slurm_Generator.sh: line 15: \n#SBATCH: command not found
Slurm_Generator.sh: line 17: \n#SBATCH: command not found
Slurm_Generator.sh: line 19: \n#SBATCH: command not found
Slurm_Generator.sh: line 21: \n#SBATCH: command not found
Slurm_Generator.sh: line 23: \n#SBATCH: command not found
Slurm_Generator.sh: line 25: \n#SBATCH: command not found
Slurm_Generator.sh: line 27: \n#SBATCH: command not found
Slurm_Generator.sh: line 30: \n: command not found
Slurm_Generator.sh: line 31: \n#ADD: command not found
Slurm_Generator.sh: line 34: \n: command not found
Slurm_Generator.sh: line 35: \nsacct: command not found

如果我运行cat -A file.sh，我会在每一行的末尾看到一个$。即使我去掉了这些，我也得到了和上面一样的结果。运行ls -al script.sh gived：-rwxrwxrwx 1 cerberus cerberus 1209 Jun 16 00:17 Slurm_Generator.sh

编辑:我将脚本更改为：

#! /bin/bash
for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)
do echo -e \
"
#\!/bin/bash
#SBATCH --partition=nonpre  # Partition (job queue)
#SBATCH --requeue              # Return job to the queue if preempted
#SBATCH --job-name=samples     # Assign a short name to your job
#SBATCH --nodes=1              # Number of nodes you require
#SBATCH --ntasks=1             # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000           # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00        # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.${FILE}.out # STDOUT output file
#SBATCH --error=slurm.%N.${FILE}.err  # STDERR output file (optional)

#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION \

sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future subm$" \
> ${FILE}.sh;
done

我的新输出如下(这要好得多)：

#\!/bin/bash
#SBATCH --partition=nonpre  # Partition (job queue)
#SBATCH --requeue           # Return job to the queue if preempted
#SBATCH --job-name=samples      # Assign a short name to your job
#SBATCH --nodes=1                 # Number of nodes you require
#SBATCH --ntasks=1                # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000              # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00           # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.Sample1.fastq.out  # STDOUT output file
#SBATCH --error=slurm.%N.Sample1.fastq.er  # STDERR output file (optional)


#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION

sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j $SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future submissions

我遇到的唯一问题是，当它打印出每个.fastq文件(这就是我想要的)时，它输出的结果.sh文件是空的。因此，它没有识别脚本的> ${File}.sh部分。

谢谢大家！

Answer 1

我意识到我必须在\之前添加一个> ${File}.sh。所以答案是：

#! /bin/bash
for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)
do echo -e \
"
#\!/bin/bash
#SBATCH --partition=nonpre  # Partition (job queue)
#SBATCH --requeue              # Return job to the queue if preempted
#SBATCH --job-name=samples     # Assign a short name to your job
#SBATCH --nodes=1              # Number of nodes you require
#SBATCH --ntasks=1             # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000           # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00        # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.${FILE}.out # STDOUT output file
#SBATCH --error=slurm.%N.${FILE}.err  # STDERR output file (optional)

#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION \

sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future subm$" \
> ${FILE}.sh;
done

Answer 2

改为使用本文档：

for FILE in *fastq; #change file type when needed (e.g., fasta, fastq, fastq.gz)
do

cat <<-EOF > ${FILE}.sh
#!/bin/bash

#SBATCH --partition=nonpre             # Partition (job queue)
#SBATCH --requeue                      # Return job to the queue if preempted
#SBATCH --job-name=samples             # Assign a short name to your job
#SBATCH --nodes=1                      # Number of nodes you require
#SBATCH --ntasks=1                     # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64             # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000                   # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00                # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.${FILE}.out  # STDOUT output file
#SBATCH --error=slurm.%N.${FILE}.err   # STDERR output file (optional)

#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION

nsacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID #this will get job run stats from SLURM; use these to help designate memory of future submissions
EOF

done