[BioC] trimTails function in ShortRead package give different results on the same input

[Zhenyu Xu]

Hi ShortRead package developer,

    I tried to use the function trimTails to trim some bad quality bases from reads coming out of 454 sequencing machine.  However I got different results if I run the command several times starting from the same ShortReadQ object and same trimming parameter. This is observed in  centos linux machine (6.2 and 6.3).  I also tried this with my own mac machine, but the results are identical. So seems the problem only restrict to centos linux machine (Not sure other linux platform has this problem or not). the data sets(~11Mb) can be downloaded at http://dl.dropbox.com/u/68829208/454reads.rds.  

best,
zhenyu

Please see the following of the execution:

wget http://dl.dropbox.com/u/68829208/454reads.rds
R

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
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> library(ShortRead)
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
> readsSub <- readRDS("454reads.rds")
> readsSub
class: ShortReadQ
length: 5460 reads; width: 5..424 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 3..416 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 3..416 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 4..424 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 5..416 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 4..424 cycles
> x = trimTails(readsSub, 20, "5", successive=TRUE)
> y = trimTails(readsSub, 20, "5", successive=TRUE)
> sum(width(x)!=width(y))
[1] 1325
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ShortRead_1.14.4    latticeExtra_0.6-19 RColorBrewer_1.0-5 
[4] Rsamtools_1.8.5     lattice_0.20-6      Biostrings_2.24.1  
[7] GenomicRanges_1.8.9 IRanges_1.14.4      BiocGenerics_0.2.0 

loaded via a namespace (and not attached):
[1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.1    hwriter_1.3    stats4_2.15.1 
[6] zlibbioc_1.2.0