[BioC] Rsamtools Error: vector of negative length

[Martin Morgan]

On 11/09/2010 06:52 AM, Christoph Bartenhagen wrote:
> Hi again,
> 
> thank you very much for your reply. It sounds very reasonable to me and
> it explains why it works with smaller BAM-files, i.e. files containing
> fewer reads.
> To track down the error, here's my sessionInfo() some more info about my
> error (I am not sure though how to generate a (small) reproducible
> example, since the problem seems to be related to quite large alignment
> files):

ok thanks for the additional info. In the mean time, a workaround is to
use the 'param' argument of scanBam to process smaller chunks (e.g.,
chromosomes) of your data at one time. Martin

> 
>> bam = scanBam(file="alignment.bam")
> Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) :
>   negative length vectors are not allowed
> 
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] Rsamtools_1.2.0     Biostrings_2.18.0   GenomicRanges_1.2.0
> [4] IRanges_1.8.0
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0
> 
> 
> My BAM-file contains 69.654.881 reads of length 36bp each.
> If this problem has already been adressed, do I need to update my
> version of Rsamtools (1.2.0)? I just saw that the release version is
> 1.2.1 and the development version is 1.3.4.
> 
> Thanks for any further advice,
> Christoph
> 
> 
> Am 09.11.2010 14:52, schrieb Martin Morgan:
>> On 11/09/2010 05:22 AM, Christoph Bartenhagen wrote:
>>   
>>> Hello everyone,
>>>
>>> I am experiencing a strange error, while reading (large) BAM-files (>
>>> 2GB) in R with the function scanBam() in the Rsamtools package.
>>> It stops saying "negative length vectors are not allowed".
>>>
>>> I think my BAM-file is ok, because I can read it in small chunks like
>>> reads on positive strand first, then reads on the negative strand (using
>>> ScanBamParam). This might be a more general Error in R because it seems
>>> to occur in very different R programs.
>>>
>>> Has anyone experienced this error?
>>> I would really appreciate any ideas how to fix this problem or
>>> concerning the reason for this error (I don't really understand what a
>>> "negative length vector" is).
>>>      
>> Hi Christoph --
>>
>> This is an integer overflow when the (accumulated) underlying DNA or
>> quality strings are too long. But I think this has been addressed and so
>> your sessionInfo() and a reproducible example (or at least the explicit
>> command that triggers the problem) would help.
>>
>> Martin
>>
>>   
>>> Thanks in advance
>>> Christoph
>>>
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>>>      
>>
>>    
> 


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