Off topic:mpileup for creating a consensus sequence

Question

[phernet123]

Dear colleagues

I desperately need your help with the samtools mpileup command. I am not variant calling, rather I want to create a consensus sequence of all the mapped reads in the Sorted.bam file. I am trying to run the following bash script:

#!/bin/bash
#PBS -l select=1:ncpus=24:mem=64GB
#PBS -P CBBI0911
#PBS -q smp
#PBS -l walltime=96:00:00
#PBS -o /mnt/lustre/users/felegbeleye/my_data/stdout.femi.txt
#PBS -e /mnt/lustre/users/felegbeleye/my_data/stderr.femi.txt
#PBS -N samtools
#PBS -M [e-mail]
module load chpc/BIOMODULES
module load samtools/0.1.19


EXE="samtools"

ARGS="mpileup -u -f 19Dec2016_S9zPn.fasta Sorted.bam |
bcftools call -c - |
vcfutils.pl vcf2fq -D 100 > femi.psmc.fq"

cd /mnt/lustre/users/felegbeleye/my_data/Ref_Genome

${EXE} ${ARGS}

---

I am getting the following error:

mpileup: invalid option -- 'c' open: No such file or directory [mpileup] failed to open |: No such file or directory

I do not have an option c in my mpileup command. My indexing of the reference was done in bwa and not in Samtools. Could that be it? I feel I am doing something basic wrong but I am new at this and would appreciate some guidance.

Thank you very much for your time and help.

Femi