[azlin]

[bwa_aln] fail to open file

hi there.
im facing a problem regarding to alignment command using bwa.

here are my command:

bwa aln -t 4 -f /media/6134b6d7-8f51-446d-9159-b10106e01d04/Postgrad/OrangAsli/KS2R/Alignment/R1_KS2R.sai hg19 /media/6134b6d7-8f51-446d-9159-b10106e01d04/Postgrad/OrangAsli/KS2R/R1_KS2R.fastq
[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 '/media/6134b6d7-8f51-446d-9159-b10106e01d04/Postgrad/OrangAsli/KS2R/R1_KS2R.fastq'. Abort!
Aborted (core dumped)


i have no idea why it was failed to open file. anyone have suggesstion?

[pd]

bwa sampe gives different output..

Hi all

I am trying to use sampe program from bwa with 3 options -P -s -a.. Here only -a option requires integer values to be provided. So how to specify these option in the command line because i tried it but i am getting different results.
Commands which i executed
a) bwa sampe -P -s -a 600
b) bwa sampe -Ps -a 600
c) bwa sampe -Psa 600

Here which one is correct? As all these commands are giving different results. Any suggestions?

[afaghalavi]

Exome sequencing

Hi

We received our exome data and now i have 2 files (snps and indels) in text format.
I paste a part of that below. Please tell me what is next stage for data analysis and what shall I do ??!!!

#$ COLUMNS seq_name pos bcalls_used bcalls_filt ref Q(snp) max_gt Q(max_gt) max_gt|poly_site Q(max_gt|poly_site) A_used C_used G_used T_used
chr1 12783 2 0 G 24 AA 5 AA 5 2 0 0 0
chr1 13057 3 1 G 3 GG 4 CG 31 0 1 2 0
chr1 13351 1 0 T 1 TT 10 GT 3 0 0 1 0
chr1 14673 2 0 G 32 CC 5 CC 5 0 2 0 0

Regards

[afaghalavi]

Hi

We received our exome data and now i have 2 files (snps and indels) in text format.
I paste a part of that below. Please tell me what is next stage for data analysis and what shall I do ??!!!

#$ COLUMNS seq_name pos bcalls_used bcalls_filt ref Q(snp) max_gt Q(max_gt) max_gt|poly_site Q(max_gt|poly_site) A_used C_used G_used T_used
chr1 12783 2 0 G 24 AA 5 AA 5 2 0 0 0
chr1 13057 3 1 G 3 GG 4 CG 31 0 1 2 0
chr1 13351 1 0 T 1 TT 10 GT 3 0 0 1 0
chr1 14673 2 0 G 32 CC 5 CC 5 0 2 0 0


Best

Afagh

[afaghalavi]

Thank you so much

[EvilTwin]

I used BWA for indexing hg19, but I had the below error !!!

afagh@afagh-VirtualBox:~$ bwa index -a bwtsw -p hg19 /mnt/desktop/hg19.fa
[bwa_index] Pack FASTA... 169.44 sec
[bwa_index] Reverse the packed sequence... Killed

Please, help me

Thank you

I once observed the same error when running bwa in a Virtual Box - Linux. No idea why. It should work if you use a non-virtual system.

[afaghalavi]

problem with BWA

I used BWA for indexing hg19, but I had the below error !!!

afagh@afagh-VirtualBox:~$ bwa index -a bwtsw -p hg19 /mnt/desktop/hg19.fa
[bwa_index] Pack FASTA... 169.44 sec
[bwa_index] Reverse the packed sequence... Killed

Please, help me

Thank you

[seq_GA]

Hi Jon,
I have been using hg18 for both aln and sampe step. I tried samse step also. I still get the segmentation fault.
I have tried using bwa-0.5.6, bwa-0.5.7 as well as from svn...

In the very firts step to convert solexa to fastq format,

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

Does it contain any bug which is causing this problem? Thanks.

[Jon_Keats]

Please forgive my ignorance but do you need to use an extension on the genome file? (ie. hg18.fa instead of hg18). In the one post you show the folder contents with hg18.fa but then in the aln and sampe commands you used hg18 alone. And are the file sizes of your .sai files the right size?

[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.

[seq_GA]

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

[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]

Thx for the info.

[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]

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.