Hello everyone,

I am fairly new to bioinformatics. I am currently learning the command line and was writing a very simple script to align multiple files (Hepatitis C viral DNA sequencing) to reference genome using BWA, and then using samtools to align to the reference.

I seem to be getting a problem in the index step.

I keep getting the same error:

[E::hts_open_format] Failed to open file HCV242.sorted.bam
samtools index: failed to open "HCV242.sorted.bam": No such file or directory

Below is the whole script:

SAMPLE_LIST="HCV176 HCV242"
for SAMPLE_ID in $SAMPLE_LIST

do
    #Index the aligner with the reference genome
    bwa index -a is HCV1.fasta
    # Align reads 1 of samples to ref genome
    bwa aln HCV1.fasta $SAMPLE_ID.1.fastq >$SAMPLE_ID.1.sai
    # Align reads 2 of samples to ref genome
    bwa aln HCV1.fasta $SAMPLE_ID.2.fastq >$SAMPLE_ID.2.sai
    # Merge and change into SAM format for both samples
    bwa sampe HCV1.fasta $SAMPLE_ID.1.sai $SAMPLE_ID.2.sai $SAMPLE_ID.1.fastq $SAMPLE_ID.2.fastq > $SAMPLE_ID.sam
    bwa sampe HCV1.fasta $SAMPLE_ID.1.sai $SAMPLE_ID.2.sai $SAMPLE_ID.1.fastq $SAMPLE_ID.2.fastq > $SAMPLE_ID.sam
    # Change the SAM to BAM format for both samples
    samtools view -bt HCV1.fasta $SAMPLE_ID.sam>$SAMPLE_ID.bam
    # Sort the BAM files
    samtools sort $SAMPLE_ID.bam -o $SAMPLE_ID.sorted
    # Create the index file for the BAM files
    samtools index -b  $SAMPLE_ID.sorted.bam
done

I've tested the code and everything works until the index command. All the necessary files are generated as expected up until that step. Any help much appreciated.