bowtie2 error "Unable to read file magic number"

Question

[rottenwasabi]

Hi, I want to create a sam file by using bowtie2. However, the "Unbale to read file magic number" error keeps showing up. I tried to unzip my reads fastq file but the error still exists. How do I fix this error?

(FYI, I am following the tutorial of InStrain, and the ultimate goal is the convert this sam file into a bam file.) This is the code from the tutorial:

`$ mkdir bt2`

`$ bowtie2-build ~/Programs/inStrain/test/test_data/N5_271_010G1_scaffold_min1000.fa bt2/N5_271_010G1_scaffold_min1000.fa`

`$ bowtie2 -p 6 -x bt2/N5_271_010G1_scaffold_min1000.fa -1 ~/Programs/inStrain/test/test_data/N5_271_010G1.R1.fastq.gz -2 ~/Programs/inStrain/test/test_data/N5_271_010G1.R2.fastq.gz > N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G1.sam`

Thank you so much!

[MatthewP]

Hello, your command has no problem. Maybe your fastq files are broken, I think you need to check the contents of fastq files.

[ATpoint]

Can you show output of:

zcat N5_271_010G1.R1.fastq.gz | head

zcat N5_271_010G1.R2.fastq.gz | head