Question: BWA - [fread] Input/output error
gravatar for egeulgen
11 months ago by
egeulgen980 wrote:

[UPDATE] So sorry to update this so late, this turned out to be an error due to a hardware issue and was fixed when the hard disk was replaced.

Hello all,

I'm trying to align paired-end read files to the reference genome using the following command (bwa version: 0.7.17-r1188):

bwa mem $ref_genome_fasta Sample_R1_001.fastq.gz Sample_R2_001.fastq.gz

I get the following error after a few seconds:

[fread] Input/output error

[UPDATE] I was thinking it might be because of an issue with the input fastq.gz files but I checked them using fqtools -validate and they seem valid.

Has anyone encountered this issue or can help me to resolve it?

bwa alignment software error • 488 views
ADD COMMENTlink modified 7 months ago • written 11 months ago by egeulgen980

You can use validateFiles from Kent utilities (linux version linked). Remember to chmod a+x validateFiles after you download the program.

$ validateFiles -type=fastq your_fastq.gz
ADD REPLYlink modified 11 months ago • written 11 months ago by genomax78k
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