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