Re: [Bio-bwa-help] bwa samse

[Neel A. <na...@wh...>]

Thanks, Martin. You are correct. I did specify "-c" but having it in the end didn't help. 


./bwa index -a is -c Danio_rerio.Zv9.61.ncrna.fa.gz[bwa_index] Pack nucleotide FASTA... 0.03 sec
[bwa_index] Convert nucleotide PAC to color PAC... 0.02 sec
[bwa_index] Reverse the packed sequence... 0.00 sec

Neel

On Mar 14, 2011, at 3:46 AM, Marcel Martin wrote:

> On Sunday 13. March 2011 04:12:54 Neel Aluru wrote:
>>> On Sat, 12 Mar 2011, Neel Aluru wrote:
>>>> I am getting an error message when I use bwa samse command. Tried with
>>>> different files and still get the same error.
>>>> 
>>>> $ ./bwa index -a is Danio_rerio.Zv9.61.ncrna.fa -c
>>>> [bwa_index] Pack FASTA... 0.01 sec
>>>> [bwa_index] Reverse the packed sequence... 0.00 sec
> 
> Are you sure you have specified the "-c" parameter for bwa index? The above 
> messages are what I get if I don't specify "-c". With "-c", the first lines 
> are:
> [bwa_index] Pack nucleotide FASTA... 0.03 sec
> [bwa_index] Convert nucleotide PAC to color PAC... 0.01 sec
> 
> Marcel
> -- 
> Dipl.-Inform. Marcel Martin, https://ls11-www.cs.tu-dortmund.de/staff/martin/
> 
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Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607