bwa question on file outputs/inputs

[ikrier]

Reposted from an old thread in the SOLiD forum :

Hi, I did the indexing with bwtsw and no -p and I got the following files :
Mouse_genome.fa.amb
Mouse_genome.fa.ann
Mouse_genome.fa.bwt
Mouse_genome.fa.pac
Mouse_genome.fa.rbwt
Mouse_genome.fa.rpac
Mouse_genome.fa.rsa
Mouse_genome.fa.sa

I managed to get the .sai file from the aln command, but now I'm stuck because the samse command gives me the error:
fail to open file '../Mouse_genome.fa.nt.ann'. Abort!

But I never get the .nt.ann file with indexing. I'm confused.

[dnusol]

Hi Ikrier,
did you manage to solve this problem? I am interested in how you got round it, because I am having problems in the previous step

I am trying to use the bwa aln command with default paramenters, I start getting lots of weird characters on the screen and finally I get no out.sai output. I get no warning that I can see.

Can anyone drop some hints?

Cheers

[ikrier]

i'm still confused because the problem solved itself. I don't even know why, but after trying several times it didn't ask for the same files anymore.

[dnusol]

Did you actually get the out.sai file in the bwa aln step?

my command is

$ ./bwa aln myref.fasta /path_to/s_1_sequence.fastq out.sai

I cannot get that out.sai file

[ikrier]

Did you try
./bwa aln myref.fasta /path_to/s_1_sequence.fastq > out.sai

[dnusol]

Shoot! I missed the >

Thanks, I'll try again

[huma Asif]

error in alignment

Dear All
while running BWA aln i got this error can anybody help in fixing it
dr@dr-Revision-A:~/Desktop/bwa-0.5.7$ ./bwa aln myref.fasta /path_to/s_1_sequence.fastq > out.sai
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_seq_open] fail to open file '/path_to/s_1_sequence.fastq'. Abort!
Aborted

Regards
Huma

[dnusol]

Hi Huma,

you actually have to write the full path to your fastq file.

So if for example you have the fastq file in

/home/huma/data/s_1_sequence.fastq

then your command should say so

./bwa aln myref.fasta /home/huma/data/s_1_sequence.fastq > out.sai

If your fastq file is in your current drectory then you don't need to specify it.

also, if you do not specify the full path where you want to redirect the output, this will be saved in the current directory

A useful trick to use is to complete the name of the files requested using the tab key. If you try to do the following from the command line

./bwa aln myref.fasta /path_to/s_1_sequence.fas [press tab to complete]

then the shell will not complete the name automatically

HTH.

[huma Asif]

use of index file in BWA

Thank you so much for your kind reply .Actually i am confused about the index files that i generated in my command
./bwa aln ref/putidaKT2440.fasta reads/pseudo.fq out.sai
I am not using index file anywhere so I am confused what do i need to do to make use of it
Regards

[huma Asif]

BWA output

finally i have run BWA aligner successfully
i have got an output file in SAM format
now i opened that sam file in samtool pseudo.bam,
pseudo.sorted.bam
pseudo.sorted.bam.bai
raw.pileup

please guide me which file shal i use to view alignment

Regards

[Orr Shomroni]

Problem solved

ikier, I had the same problem as you with the core dumped and the fa.nt.ann failure to open. I found the solution. When you run the bwa index, it should be run with the following code:

bwa index -a bwtsw database.fasta

For some reason, bwa index by default uses algorithm IS, which doesn't work as well as the BWTSW algorithm. See the explanation on the website

http://bio-bwa.sourceforge.net/bwa.shtml

[dtc]

Hi Ikrier,
do you know how it fixed itself now,I have the same problem,but I tried many times,it still can't work.
Cheers

[swbarnes2]

ikier, I had the same problem as you with the core dumped and the fa.nt.ann failure to open. I found the solution. When you run the bwa index, it should be run with the following code:

bwa index -a bwtsw database.fasta

For some reason, bwa index by default uses algorithm IS, which doesn't work as well as the BWTSW algorithm. See the explanation on the website

http://bio-bwa.sourceforge.net/bwa.shtml

The default index on bwa index works fine for small genomes. I use all the time with no problems on bacterial genomes.

But for larger genomes, like mammals, yes, you have to use bwtsw.