Manta "--exome: command not found"

Question

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

Answer 1

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 {} \;