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.
>
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