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

Michael Muratet mmuratet at hudsonalpha.org
Thu Nov 12 23:48:32 CET 2009


I have a version of Rolexa I have modified to operate with versions  
1.3+ of the Illumina pipeline (i.e., *.cif files). I'm running this  
with the development version of R and a version of ShortRead that I  
also modified to work with versions 1.3+ of the Illumina pipeline. I  
am trying to run the batch version of Rolexa thusly:



rolenv.1 = SetModel()
sp.1 <- SolexaPath("/data/illumina_ga/090829_HWI-EAS295_42RYTAAXX")

ForkBatch(run=rolenv.1, sp.1, outpath="./", prefix="rs.1", nthreads=2,  
nfiles=2, lane=lane, tiles=1:2)

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) 
        cycles = 1:ncycles)
8: SeqScore(run = run, int = int, seqInit = seq, colonies = 1:dim(int) 
        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?

Session info is below if anyone would like to speculate about the  
source of the problem.



 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-09 r49643)

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rolexa_1.0.5      ShortRead_1.5.0   lattice_0.17-25    
[5] Biostrings_2.15.0 IRanges_1.5.0     mclust_3.3.2      fork_1.2.2

loaded via a namespace (and not attached):
[1] Biobase_2.6.0 grid_2.10.0   hwriter_1.1

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806

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