BWA error

[seq_GA]

I am trying to map solexa pair end reads using BWA.
1. As the first step, I converted solexa fastq format into sanger fastq using maq.

maq-0.7.1/maq sol2sanger s_5_2_sequence.txt s_5_2_fastq.txt

2. I build the indices for BWA for human genome

BWA/bwa-0.5.6/bwa index -a bwtsw -p hg18 hg18.fa

3. Next step is to generate suffice array coordiantes for read1 as below:

 BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18.fa s_5_1_fastq.txt > s_5_1.sai

I am getting error as below.

[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
[bwt_restore_bwt] fail to open file '/BWA/Genomes/hg18/hg18.fa.bwt'. Abort!
Aborted

I have all the fasta as well as built indices under the same directory as below:
hg18.fa
hg18.pac
hg18.ann
hg18.amb
hg18.rpac
hg18.bwt
hg18.rbwt
hg18.sa
hg18.rsa

Anything wrong with this or do I have to move hg18.fa out of this directory? Thanks.

[nilshomer]

If you used "hg18" as your prefix in your "bwa index" step, you should use the same prefix in your "bwa aln" step:

 BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_1_fastq.txt > s_5_1.sai

Ideally, you would not specify "-p" (unless of course you use both Illumina and ABI SOLiD data).

[seq_GA]

Thanks and it works.

[seq_GA]

For a pair end read, I tried as below:

BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_1_fastq.txt > s_5_1.sai
BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_2_fastq.txt > s_5_2.sai

BWA/bwa-0.5.6/bwa sampe BWA/Genomes/hg18/hg18 s_5_1.sai s_5_2.sai s_5_1_fastq.txt s_5_2_fastq.txt > out.sam

I get the following error:

[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
 Segmentation fault

How to resolve the issue? Thanks.

[nilshomer]

For a pair end read, I tried as below:

BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_1_fastq.txt > s_5_1.sai
BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_2_fastq.txt > s_5_2.sai

BWA/bwa-0.5.6/bwa sampe BWA/Genomes/hg18/hg18 s_5_1.sai s_5_2.sai s_5_1_fastq.txt s_5_2_fastq.txt > out.sam

I get the following error:

[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...

How to resolve the issue? Thanks.

What's the error (the above is a status message)? Did it not finish?

[seq_GA]

I was trying to edit my post.. You are too fast.. Anyway I get segmentation fault. Thanks.

[nilshomer]

I was trying to edit my post.. You are too fast.. Anyway I get segmentation fault. Thanks.

Sounds like a bug. Did you try sending an email to the BWA mailing list or author (lh3 is his handle on seqanswers)?

[seq_GA]

I am not able to join the mailing list and post because of some error.
I am trying to contenate all fasta of hg18 as hg18.fa and then build index. Anything wrong in that approach?

[drio]

I am not able to join the mailing list and post because of some error.
I am trying to contenate all fasta of hg18 as hg18.fa and then build index. Anything wrong in that approach?

You are using an old version of bwa. Please update to -svn or get the latest release.

[seq_GA]

Hi,
Thx for the response. I am using bwa-0.5.6 and I am upgrading to latest version available bwa-0.5.7. How to check out the version from svn? Can you please provide me the link? Thanks.

[nilshomer]

Hi,
Thx for the response. I am using bwa-0.5.6 and I am upgrading to latest version available bwa-0.5.7. How to check out the version from svn? Can you please provide me the link? Thanks.

Here's the command. Make sure you have subversion installed:

svn co http://bio-bwa.svn.sourceforge.net/svnroot/bio-bwa bio-bwa

[seq_GA]

Thx for the info.

[drio]

Hi,
Thx for the response. I am using bwa-0.5.6 and I am upgrading to latest version available bwa-0.5.7. How to check out the version from svn? Can you please provide me the link? Thanks.

If you want to avoid svn (I'd suggest you don't), from here:

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

click in SF download page. That will take you to the latest release (already binary).

ALso, perhaps you can tell Heng how you got to the older version. I think there are some links there that still point to old versions.

[seq_GA]

Hi,
i get the same error even if I use the build from svn..

[drio]

Run your binary via gdb:

$ gdb your_bwa_binary
.... gdb output ... 
> run sampe BWA/Genomes/hg18/hg18 s_5_1.sai s_5_2.sai s_5_1_fastq.txt s_5_2_fastq.txt > out.sam
.... gdb output ....
> bt

And show us the output.