Deconseq database generation issues

Question

[julestrachsel]

Hello!

I am attempting to remove host cell line reads from viral reads for a viral genome sequencing effort. (Miseq 2x300 Nextera). I downloaded and set up deconseq according to the install file, and generated a database using bwa64 on my desired genome. This worked great and I was able to filter the host genomic reads from my viral reads. I used velvet to assemble my clean viral reads and everything looked good. I blasted my resulting contigs and discovered that the host cell mitochondrial DNA reads had not been filtered out. I attempted to generate a new database with a mitochondrial genome I got from genbank. I used a nearly identical command to generate this new database but it would fail to create all 8 necessary files. I would only ever get 4. The .amb .ann .pac .rpac files are generated but not the .bwt .rbwt .sa .rsa files.

This is the command I used:

bwa64 index -p dogmito -a bwtsw ~/deconseq-standalone-0.4.3/db/dogmito.fna > out.txt 2>&1

The out.txt file reads

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Reverse the packed sequence... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...

Additionally I noticed that when I typed ls to see if the files had been generated I got the following message:

[1]+  Segmentation fault      (core dumped) bwa64 index -p dogmito -a bwtsw ~/deconseq-standalone-0.4.3/db/dogmito.fna > out.txt 2>&1

I've looked through my mitochondrial genome fasta and I can't see anything out of the ordinary .

Any idea what I'm doing wrong?

Thanks!!

Answer 1

[5heikki]

bwtsw is only for large genomes..see Simple Question: What Is "Large" For Bwa?

[julestrachsel]

Thank you!

I really should have learned more about bwa first. I used -a is in my database generation command on the mitochondrial genome and it worked like a dream.

Thanks again!!