[BioC] Genominator error when calling syste.time

[Kasper Daniel Hansen]

On Thu, Apr 12, 2012 at 11:15 AM, Boel Brynedal <Boel.Brynedal at ki.se> wrote:
> I have 12 GB of RAM for this job, and the BAM files are not particularly big. Is it likely that this is a memory issue? I'm writing the files in my own folder on a larger cluster, so there should not be a problem with permissions. Or? How can I investigate whether this is a permission issue?
>
> Changing the names of aligned did get rid of the warning however.
>
>> eData <- importFromAlignedReads(aligned, dbFilename='/fg/cogdec/Boel/Marga/test/test.db',tablename='raw',type="BAM")
> Error in match(chromosome(aln), chrMap) :
>  error in evaluating the argument 'table' in selecting a method for function 'match': Error: argument "chrMap" is missing, with no default
> Timing stopped at: 6.628 0.001 6.63

You are missing the chrMap=chroms you use below.

> On my MacBook pro I am able to get this function to work (same packages, using R.12.)
>
> Using R.12.1 on the cluster I get:
>
>> eData <- importFromAlignedReads(aligned, chrMap=chroms,dbFilename='test.db',tablename='raw',type="BAM")
> Error in system.time(exp) :
>  Unable to write the table, delete table or specify overwrite.
> In addition: Warning message:
> In value[[3L]](cond) :
>  RS-DBI driver: (error in statement: near ".6": syntax error)
> Timing stopped at: 0.053 0.001 0.056
> Timing stopped at: 12.552 0.633 13.228
>

The names of the columns in the table has to by valid names according
to the SQL syntax.  This precludes the use of *.*.  Instead of
renaming the files you could so something like

  names(aligned) = c("sample1", "sample2", ...)

then the column names will be the names of the aligned vector.

Kasper

> Any suggestions highly appreciated!
> Boel
>
>
> ________________________________________
> From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com]
> Sent: Wednesday, April 11, 2012 3:57 PM
> To: Dan Tenenbaum
> Cc: Boel Brynedal; bioconductor at r-project.org; James Bullard
> Subject: Re: [BioC] Genominator error when calling syste.time
>
> Sounds reasonable, probably because the column names will start with numbers.
>
> Kasper
>
> On Wed, Apr 11, 2012 at 3:46 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> [CC'ing Genominator maintainer]
>>
>> On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at gmail.com> wrote:
>>> On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <Boel.Brynedal at ki.se> wrote:
>>>>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE)
>>>> Error in system.time(exp) :
>>>>  Unable to write the table, delete table or specify overwrite.
>>>> In addition: Warning message:
>>>> In value[[3L]](cond) :
>>>>  RS-DBI driver: (error in statement: near "20417.6": syntax error)
>>>> Timing stopped at: 0.076 0 0.081
>>>> Timing stopped at: 12.851 0.74 13.631
>>>
>>> The system.time is a red herring I think.  Note that it says
>>>  >  Unable to write the table, delete table or specify overwrite.
>>> I suggest you have too little disk space, or permission issues.
>>>
>>
>> It seems that the warning is significant as well. Looks like the
>> package is trying to use the names of your BAM files in a SQL query
>> but that query is malformed.
>>
>> Dan
>>
>>
>>> Kasper
>>>
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