Question: BWA alignment error
gravatar for alhafidzhamdan
12 days ago by
alhafidzhamdan0 wrote:

Hi there,

I have searched throughout the site and I still can't find an answer. I have ref genome hg38.fa and bwa index files in the same directory/folder I am trying to align a fastq file but it keeps returning this

[M::bwa_idx_load_from_disk] read 0 ALT contigs [fread] Unexpected end of file

I have tried re-indexing, and re-downloading the fastq files. Still the same error. Is it a problem of directory?

bwa alignment assembly • 86 views
ADD COMMENTlink written 12 days ago by alhafidzhamdan0

Share the full command line output including the command you are using for alignment.

ADD REPLYlink modified 12 days ago • written 12 days ago by arup1.5k

Looks like your index are corrupted, better if you generate a new ones

ADD REPLYlink written 12 days ago by JC8.2k
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