<p>You're missing a <code>\</code> in the line before the one containing the <code>--exome</code>, so shell treats it as a new command, which is why you see this error. Add the <code> \</code> after <code>${sub_dir}</code> and your script should not give you this error.</p>
<p>With that correction added in, your code will look like:</p>
<pre><code># Accept path to reference fasta file as a parameter:

reference=$1

# Accept input and output directories as parameters:

input_dir=$2

output_dir=$3

# Hard coded Manta Installation Path:

## If someone installs Manta they must specify where the installation is placed:

MANTA_INSTALL_PATH=&quot;/path/to/manta-1.6.0.release_src/install&quot;


# Main code:
for file in <span class="math-container">${input_dir}/*.bam
do
  # Create subdirectory named after bam file
  sub_dir=$</span>{output_dir}/<span class="math-container">$(basename $</span>{file} .bam)
  mkdir -p ${sub_dir}

  # Use reference fasta path specified by user
  <span class="math-container">${MANTA_INSTALL_PATH}/bin/configManta.py \
    --bam $</span>file \
    --referenceFasta <span class="math-container">${reference} \
--runDir $</span>{sub_dir} \
    --exome
done

# Now run each `runWorkflow.py`

find &quot;$output_dir&quot; -name &quot;runWorkflow.py&quot; -exec {} \;
</code></pre>

CC BY-SA 4.0
2023-03-28T22:01:29.590Z
Thank you Ram. I edited the code above to reflect the change you suggested.
Indira
CC BY-SA 4.0
2023-03-29T01:44:35.650Z
@Indira I think this should have been the accepted answer. Do you still get the error `--exome: command not found` or something else?
Steve
CC BY-SA 4.0
2023-03-29T15:52:09.277Z
@Indira Did you or did you not run the original command with the backslash? The answer was to your question, not a correction to a typo in your post.
Ram RS
CC BY-SA 4.0
2023-03-29T21:40:29.607Z
I did run the original commands with a backslash and it did work. Thank you.
Indira
CC BY-SA 4.0
2023-03-29T21:55:17.557Z
In that case, you should have accepted the answer, not changed the question.
Ram RS
CC BY-SA 4.0
2023-03-29T22:01:13.783Z
I accept the answer, and I changed the code in the question to reflect the correct code that should be used.
Indira
CC BY-SA 4.0
2023-03-29T22:02:02.160Z
That is not how forums work. You let the question have the wrong code and the answer shows the correction. That way, other that made the mistake can figure out the change to be made to their code. I've reversed your edit, accept the answer please.
Ram RS
CC BY-SA 4.0
2023-03-29T22:02:42.937Z
Oh I will try and keep that in mind for my next post.
Indira
CC BY-SA 4.0
2023-03-29T22:22:26.677Z
@M__ can you clean up the comments please?
Ram RS
CC BY-SA 4.0
2023-03-28T18:27:16.613Z
2023-03-29T22:16:09.300Z
2023-03-29T22:16:09.300Z
Ram RS
<p>I am using Manta (<a href="https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md" rel="nofollow noreferrer">https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md</a>) but whenever I try to specify the <code>--exome</code> command using the following code I get the error below:</p>
<p>The code in my script:</p>
<pre><code># Accept path to reference fasta file as a parameter:

reference=$1

# Accept input and output directories as parameters:

input_dir=$2

output_dir=$3

# Hard coded Manta Installation Path:

## If someone installs Manta they must specify where the installation is placed:

MANTA_INSTALL_PATH=&quot;/path/to/manta-1.6.0.release_src/install&quot;


# Main code:
for file in <span class="math-container">${input_dir}/*.bam
do
  # Create subdirectory named after bam file
  sub_dir=$</span>{output_dir}/<span class="math-container">$(basename $</span>{file} .bam)
  mkdir -p ${sub_dir}

  # Use reference fasta path specified by user
  <span class="math-container">${MANTA_INSTALL_PATH}/bin/configManta.py \
    --bam $</span>file \
    --referenceFasta <span class="math-container">${reference} \
--runDir $</span>{sub_dir}
    --exome
done

# Now run each `runWorkflow.py`

find &quot;$output_dir&quot; -name &quot;runWorkflow.py&quot; -exec {} \;
</code></pre>
<p>The <code>runDir</code> is directly below the previous command however, it doesn't seem to write well in this post.</p>
<p>I ran the script via the following command:</p>
<pre><code>./script.sh /path/to/reference.fa /path/to/bam_files /path/to/output_dir
</code></pre>
<p>I get the error:</p>
<pre><code>/path/to/my/sample/folder/sample1/runWorkflow.py
/path/to/this/job_scripts/number_by_HPC: line 40: --exome: command not found
</code></pre>
<p>How do I get it to run with the <code>--exome</code> command and not get the following error (it works without the <code>--exome</code> command)? I am using exome data so I believe I need to use the <code>--exome</code> command</p>

<bash><exome>
Manta "--exome: command not found"
# Manta "--exome: command not found"

(Asked by: username_0 on 2023-03-28)

I am using Manta (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the --exome command using the following code I get the error below:
The code in my script:
# Accept path to reference fasta file as a parameter:

reference=$1

# Accept input and output directories as parameters:

input_dir=$2

output_dir=$3

# Hard coded Manta Installation Path:

## If someone installs Manta they must specify where the installation is placed:

MANTA_INSTALL_PATH="/path/to/manta-1.6.0.release_src/install"


# Main code:
for file in ${input_dir}/*.bam
do
  # Create subdirectory named after bam file
  sub_dir=${output_dir}/$(basename ${file} .bam)
  mkdir -p ${sub_dir}

  # Use reference fasta path specified by user
  ${MANTA_INSTALL_PATH}/bin/configManta.py \
    --bam $file \
    --referenceFasta ${reference} \
--runDir ${sub_dir}
    --exome
done

# Now run each `runWorkflow.py`

find "$output_dir" -name "runWorkflow.py" -exec {} \;

The runDir is directly below the previous command however, it doesn't seem to write well in this post.
I ran the script via the following command:
./script.sh /path/to/reference.fa /path/to/bam_files /path/to/output_dir

I get the error:
/path/to/my/sample/folder/sample1/runWorkflow.py
/path/to/this/job_scripts/number_by_HPC: line 40: --exome: command not found

How do I get it to run with the --exome command and not get the following error (it works without the --exome command)? I am using exome data so I believe I need to use the --exome command

**Tags:** bash, exome

---

## 1 answers

### Answer by username_1 on 2023-03-28. Score: 4 | Accepted answer

You're missing a \ in the line before the one containing the --exome, so shell treats it as a new command, which is why you see this error. Add the  \ after ${sub_dir} and your script should not give you this error.
With that correction added in, your code will look like:
# Accept path to reference fasta file as a parameter:

reference=$1

# Accept input and output directories as parameters:

input_dir=$2

output_dir=$3

# Hard coded Manta Installation Path:

## If someone installs Manta they must specify where the installation is placed:

MANTA_INSTALL_PATH="/path/to/manta-1.6.0.release_src/install"


# Main code:
for file in ${input_dir}/*.bam
do
  # Create subdirectory named after bam file
  sub_dir=${output_dir}/$(basename ${file} .bam)
  mkdir -p ${sub_dir}

  # Use reference fasta path specified by user
  ${MANTA_INSTALL_PATH}/bin/configManta.py \
    --bam $file \
    --referenceFasta ${reference} \
--runDir ${sub_dir} \
    --exome
done

# Now run each `runWorkflow.py`

find "$output_dir" -name "runWorkflow.py" -exec {} \;

> **Comments:**
> **username_0**: Thank you Ram. I edited the code above to reflect the change you suggested.  
> **username_2**: @Indira I think this should have been the accepted answer. Do you still get the error `--exome: command not found` or something else?  
> **username_1**: @Indira Did you or did you not run the original command with the backslash? The answer was to your question, not a correction to a typo in your post.  
> **username_0**: I did run the original commands with a backslash and it did work. Thank you.  
> **username_1**: In that case, you should have accepted the answer, not changed the question.  
> **username_0**: I accept the answer, and I changed the code in the question to reflect the correct code that should be used.  
> **username_1**: That is not how forums work. You let the question have the wrong code and the answer shows the correction. That way, other that made the mistake can figure out the change to be made to their code. I've reversed your edit, accept the answer please.  
> **username_0**: Oh I will try and keep that in mind for my next post.  
> **username_1**: @M__ can you clean up the comments please?  

---

