[Bioc-sig-seq] Rolexa run-time error in batch mode

[Michael Muratet]

On Nov 12, 2009, at 5:19 PM, Seth Falcon wrote:

> Hi Michael,
>
> Sorry I don't have more, but a few hints are below...
>
> On 11/12/09 2:48 PM, Michael Muratet wrote:
>> which grinds along for awhile and then I get a "subscript out of  
>> bounds"
>> error in a method with which I am unfamiliar. See traceback:
>>
>> > traceback()
>> 18: stop("subscript out of bounds")
>> 17: .nextMethod(x = x, i = i, ...)
>> 16: .Call("R_nextMethodCall", call, callEnv, PACKAGE = "methods")
>> 15: callNextMethod()
>> 14: x at ranges[i]
>> 13: x at ranges[i]
>> 12: seqInit at sread[colonies]
>> 11: seqInit at sread[colonies]
>> 10: .local(run, ...)
>> 9: SeqScore(run = run, int = int, seqInit = seq, colonies =  
>> 1:dim(int)[1],
>> cycles = 1:ncycles)
>> 8: SeqScore(run = run, int = int, seqInit = seq, colonies =  
>> 1:dim(int)[1],
>> cycles = 1:ncycles)
>> 7: .local(run, ...)
>> 6: OneBatch(run, path, lane, tiles[fn + 1:nfiles], outpath, prefix)
>> 5: OneBatch(run, path, lane, tiles[fn + 1:nfiles], outpath, prefix)
>> 4: ForkBatch(run = rolenv.1, sp.1, outpath = "./", prefix = "rs.1",
>> nthreads = 2, nfiles = 2, lane = lane, tiles = 1:2)
>> 3: eval.with.vis(expr, envir, enclos)
>> 2: eval.with.vis(ei, envir)
>> 1: source("batch_analysis.R")
>>
>> I haven't been able to locate the method where the error occurs.  
>> Maybe
>> it's in R itself somewhere. Can anyone point me in the right  
>> direction?
>
> Frames 11, 12 are from the Rolexa package, I believe.  Line 213 of  
> Rolexa/R/Model.R has:
>
>                      siseq = seqInit at sread[colonies]
>
> Then frames 13, 14 jump to either IRanges or Biostrings code (or  
> both).
>
> Have you been able to run a perhaps smaller example without the fork  
> package?
Seth

Yes, I am able to execute the process manually. I will take a look at  
it again this morning and if I can figure it out I will write a script  
to do it manually and serially.

Thanks

Mike
>
> I'm not familiar with fork, but assuming that it is forking the R  
> process, one might be suspicious of using fork with packages that  
> use external pointers such as Biostrings.  Since R is not multi- 
> threaded, package code is not setup for concurrent access... Or this  
> might have nothing to do with the issue you are seeing :-P
>
> + seth
>
> -- 
> Seth Falcon
> Program in Computational Biology | Fred Hutchinson Cancer Research  
> Center

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
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(256) 327-0966 (f)

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