Question: Deconseq database generation issues
1
gravatar for julestrachsel
3.9 years ago by
United States
julestrachsel20 wrote:

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!!

 

 

 

ADD COMMENTlink modified 3.9 years ago by 5heikki8.4k • written 3.9 years ago by julestrachsel20
3
gravatar for 5heikki
3.9 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:
bwtsw is only for large genomes..see Simple Question: What Is "Large" For Bwa?
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by 5heikki8.4k
1

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!!

 

ADD REPLYlink written 3.9 years ago by julestrachsel20
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