Question: Error with samtools index command
0
owenz • 10 wrote:
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.
Thanks for your reply. I didn't seem to notice this little detail
The issue has been fixed
Details always matter in bioinformatics :-)
You should
acceptthe answers below since they solved your problem.