Burrows-Wheeler Aligner

When run it separately, it is ok. So bwa0.6.0 bwasw still cannnot work
for paired-end data?

~/bin/bwa-0.6.0/bwa bwasw
~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
1.fq > a.sam
[bsw2_aln] read 74999 sequences/pairs (7295164 bp)...
[main] Version: 0.6.0-r102-dev
[main] CMD: ~/bin/bwa-0.6.0/bwa bwasw
~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
1.fq
[main] Real time: 43.145 sec; CPU: 41.747 sec

 ~/bin/bwa-0.6.0/bwa bwasw
~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
2.fq > b.sam
[bsw2_aln] read 74999 sequences/pairs (7375548 bp)...
[main] Version: 0.6.0-r102-dev
[main] CMD: ~/bin/bwa-0.6.0/bwa bwasw
~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
2.fq
[main] Real time: 43.816 sec; CPU: 42.051 sec

On Thu, Nov 24, 2011 at 11:46 PM, Heng Li <lh3@...> wrote:
> Thanks for your example. Does these files cause segfault for your reference genome? Unfortunately, as I tried here, bwasw does not segfault. Even valgrind complains nothing. Thus I may not be able to fix this bug. I will wait to see if other users have the same issue.
>
> Thanks anyway,
>
> Heng
>
>
> On Nov 24, 2011, at 4:16 AM, Jinyan Huang wrote:
>
>> Heng,
>>
>> The attachments are the fq files.
>>
>> The command is:
>>
>> /env/tongji/home/jhuang/bin/bwa-0.6.0/bwa bwasw
>> /env/tongji/home/jhuang/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
>> test/1.fq test/2.fq > test/7010_4.sam
>>
>> On Thu, Nov 24, 2011 at 11:25 AM, Heng Li <lh3@...> wrote:
>>> Could you find the batch of reads that lead to the segfault? It is nearly impossible to find the cause simply from the log file. You may get ~20Mbp reads around the following the last reported alignment and see if those reads lead to segfault. If yes, please let me know. Thanks.
>>>
>>> Heng
>>>
>>> On Nov 22, 2011, at 5:45 AM, Jinyan Huang wrote:
>>>
>>>> Dear li,
>>>>
>>>> your new version can fix the most of Segmentation fault for my
>>>> samples. But for one sample, it still has this problem. Segmentation
>>>> fault      (core dumped)
>>>>
>>>> ~/bin/bwa-0.6.0/bwa bwasw
>>>> ~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
>>>> mapping/myread_3/myread_3_1.fq mapping/myread_3/myread_3_2.fq >
>>>> ~/rna-seq/exp/data/bwa06//myread_3.sam
>>>> [bsw2_aln] read 102734 sequences/pairs (10000150 bp)...
>>>> /bin/bash: line 1: 11756 Segmentation fault      (core dumped)
>>>> ~/bin/bwa-0.6.0/bwa bwasw
>>>> ~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
>>>> mapping/myread_3/myread_3_1.fq mapping/myread_3/myread_3_2.fq >
>>>> ~/rna-seq/exp/data/bwa06//myread_3.sam
>>>
>>>
>>>
>>> --
>>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>>  Limited, a charity registered in England with number 1021457 and a
>>>  company registered in England with number 2742969, whose registered
>>>  office is 215 Euston Road, London, NW1 2BE.
>>>
>> <fq1.tar.gz><fq2.tar.gz>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>

Could you compile with "make CFLAGS=-g" and run:

valgrind bwa bwasw ref.fa 1.fq 2.fq 

for me? I guess this may be because the difference genome sequences you are using. Most Linux distribution has the valgrind package. This command line may take a couple of hours as valgrind will slow programs slow by a factor of 10.

Thanks,

Heng

On Nov 25, 2011, at 10:33 PM, Jinyan Huang wrote:

> Yes. With this fq files. I constantly get follow error:
> 
> bwa is from: https://nodeload.github.com/lh3/bwa/zipball/master
> 
> ~/bin/bwa-0.6.0/bwa bwasw
> ~/bin/genome_index/reference_genomes/Homo_sapiens.GRCh37.63/bwa06/Homo_sapiens.GRCh37.63.dna.chromosome.fa
> 1.fq 2.fq > 7010_4.sam
> [bsw2_aln] read 102790 sequences/pairs (10000146 bp)...
> *** glibc detected *** ~/bin/bwa-0.6.0/bwa: free(): invalid next size
> (fast): 0x000000000405ca50 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0x7f7e4701b9a8]
> /lib/libc.so.6(cfree+0x76)[0x7f7e4701dab6]
> ~/bin/bwa-0.6.0/bwa[0x42ab3e]
> ~/bin/bwa-0.6.0/bwa[0x42b476]
> ~/bin/bwa-0.6.0/bwa[0x42539e]
> ~/bin/bwa-0.6.0/bwa[0x4275c8]
> ~/bin/bwa-0.6.0/bwa[0x427857]
> ~/bin/bwa-0.6.0/bwa[0x422a68]
> ~/bin/bwa-0.6.0/bwa[0x42bedd]
> /lib/libc.so.6(__libc_start_main+0xe6)[0x7f7e46fc61a6]
> ~/bin/bwa-0.6.0/bwa[0x401a49]
> ======= Memory map: ========
> 00400000-00433000 r-xp 00000000 00:13 4551233577
>  ~/bin/bwa-0.6.0/bwa
> 00633000-00636000 rw-p 00033000 00:13 4551233577
>  ~/bin/bwa-0.6.0/bwa
> 018bf000-0408f000 rw-p 018bf000 00:00 0                                  [heap]
> 7f7cfc000000-7f7cfc021000 rw-p 7f7cfc000000 00:00 0
> 7f7cfc021000-7f7d00000000 ---p 7f7cfc021000 00:00 0
> 7f7d0376e000-7f7d03784000 r-xp 00000000 fe:00 219027
>  /lib/libgcc_s.so.1
> 7f7d03784000-7f7d03984000 ---p 00016000 fe:00 219027
>  /lib/libgcc_s.so.1
> 7f7d03984000-7f7d03985000 rw-p 00016000 fe:00 219027
>  /lib/libgcc_s.so.1
> 7f7d03985000-7f7d03e86000 rw-p 7f7d040de000 00:00 0
> 7f7d04096000-7f7e46fa8000 rw-p 7f7d04096000 00:00 0
> 7f7e46fa8000-7f7e470f2000 r-xp 00000000 fe:00 221134
>  /lib/libc-2.7.so
> 7f7e470f2000-7f7e472f1000 ---p 0014a000 fe:00 221134
>  /lib/libc-2.7.so
> 7f7e472f1000-7f7e472f4000 r--p 00149000 fe:00 221134
>  /lib/libc-2.7.so
> 7f7e472f4000-7f7e472f6000 rw-p 0014c000 fe:00 221134
>  /lib/libc-2.7.so
> 7f7e472f6000-7f7e472fb000 rw-p 7f7e472f6000 00:00 0
> 7f7e472fb000-7f7e47311000 r-xp 00000000 fe:00 221145
>  /lib/libpthread-2.7.so
> 7f7e47311000-7f7e47511000 ---p 00016000 fe:00 221145
>  /lib/libpthread-2.7.so
> 7f7e47511000-7f7e47513000 rw-p 00016000 fe:00 221145
>  /lib/libpthread-2.7.so
> 7f7e47513000-7f7e47517000 rw-p 7f7e47513000 00:00 0
> 7f7e47517000-7f7e4752d000 r-xp 00000000 fe:01 421849
>  /usr/lib/libz.so.1.2.3.3
> 7f7e4752d000-7f7e4772d000 ---p 00016000 fe:01 421849
>  /usr/lib/libz.so.1.2.3.3
> 7f7e4772d000-7f7e4772e000 rw-p 00016000 fe:01 421849
>  /usr/lib/libz.so.1.2.3.3
> 7f7e4772e000-7f7e477b0000 r-xp 00000000 fe:00 221126
>  /lib/libm-2.7.so
> 7f7e477b0000-7f7e479af000 ---p 00082000 fe:00 221126
>  /lib/libm-2.7.so
> 7f7e479af000-7f7e479b1000 rw-p 00081000 fe:00 221126
>  /lib/libm-2.7.so
> 7f7e479b1000-7f7e479cd000 r-xp 00000000 fe:00 221141
>  /lib/ld-2.7.so
> 7f7e479e0000-7f7e47bba000 rw-p 7f7e479e0000 00:00 0
> 7f7e47bc9000-7f7e47bcc000 rw-p 7f7e47bc9000 00:00 0
> 7f7e47bcc000-7f7e47bce000 rw-p 0001b000 fe:00 221141
>  /lib/ld-2.7.so
> 7fff7e01f000-7fff7e035000 rw-p 7ffffffe8000 00:00 0                      [stack]
> 7fff7e1d2000-7fff7e1d3000 r-xp 7fff7e1d2000 00:00 0                      [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>  [vsyscall]
> Aborted



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.