Hi Sung-Huan,
Upon further inspection, your BAM file is actually a bit malformed (you can
get around this with the --ignore-RG option, but you shouldn't have to).
The problem is that the auxiliary data is set as being larger than needed
and so skip_aux ends up finding a bunch of nulls, which cause it to abort.
Interestingly, this is still the case if remake the BAM file after
converting to a proper SAM file, so there is a bug here, just not one
directly in the mpileup code.
I'll look into this a bit more since, if correct, it would seem like this
would affect a lot of the rest of us too.
Best,
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<[email protected]>
On Mon, Sep 22, 2014 at 12:08 PM, Sung-Huan Yu <
[email protected]> wrote:
> Hi,
>
> I already uploaded the genome fasta file here.
>
> https://data.imib-zinf.net/Staphylococcus_aureus_HG003.zip
>
> please refer to it.
>
> Best,
>
> Sung-Huan
>
>
> Quoting Devon Ryan <[email protected]>:
>
> Hi Sung-Huan,
>>
>> At least on my laptop I can't reproduce this (I get the expected bcf file
>> output), though since I don't have your fasta file perhaps that's why.
>> Could you post that somewhere as well?
>>
>> Best,
>> Devon
>>
>> ____________________________________________
>> Devon Ryan, Ph.D.
>> Email: [email protected]
>> Tel: +49 (0)178 298-6067
>> Molecular and Cellular Cognition Lab
>> German Centre for Neurodegenerative Diseases (DZNE)
>> Ludwig-Erhard-Allee 2
>> 53175 Bonn, Germany
>>
>> On Sep 19, 2014, at 2:19 PM, Sung-Huan Yu wrote:
>>
>> Dear all,
>>>
>>> I would like to use samtools to call SNP. I use the latest version 1.0.
>>> First, I have to generate bcf file.
>>> I run the following command.
>>>
>>> samtools mpileup -t DP -ugf my.fasta my.bam
>>>
>>> the result is always like this:
>>>
>>> [mpileup] 1 samples in 1 input files
>>> Set max per-file depth to 8000
>>> Aborted
>>>
>>> If I just run
>>>
>>> samtools mpileup -f my.fasta my.bam
>>>
>>> it works fine.
>>> I have no idea what happens.
>>> If I go back to use samtools-0.1.19 to run
>>>
>>> samtools mpileup -uD -f my.fasta my.bam
>>>
>>> everything is okay.
>>> Could anyone helps me? Thank you.
>>>
>>> I also parsed the BAM file to short one. I found when the line comes to
>>> 88, it will aborted. Before line 88, everythin is fine. But I checked the
>>> file, I didn't see anything wrong. Please refer the attachment.
>>> Sung-Huan
>>>
>>>
>>> <short.bam>-------------------------------------------------
>>> -----------------------------
>>> Slashdot TV. Video for Nerds. Stuff that Matters.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=160591471&;
>>> iu=/4140/ostg.clktrk_______________________________________________
>>> Samtools-help mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>>
>>
>>
>>
>
>
>
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