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.