[BioC] Genominator error when calling syste.time

[Boel Brynedal]

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 

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 

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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor