[Bioc-sig-seq] qa error in ShortRead

[Kunbin Qu]

Hi, 

I received the following error when I tried to read some fastq in and
generate QA report. Could anybody help me? Thanks.

-Kunbin


[srp101]more tmp2
@SEQUENCER01_0007:1:1:1066:13331#0/1
CAGCTANCTGCGTTCTTCATCGACGCACGAGCCGAGTATTAATGTGAATTG
+SEQUENCER01_0007:1:1:1066:13331#0/1
fdfffcBccccccccfffffffeffffffcfffffedcfcffffddedfdd
@SEQUENCER01_0007:1:1:1066:8699#0/1
CTTACCNCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCAC
+SEQUENCER01_0007:1:1:1066:8699#0/1
cc^ccaBV]]ba_^Zc^cbaa`c`cL^```cb\ccc^aaaaa^aabba`bb
@SEQUENCER01_0007:1:1:1066:20185#0/1
GCCACANACACCTGATTATCAACAGCCCGGCTTCGCTGAAGTAACTCCCAA
+SEQUENCER01_0007:1:1:1066:20185#0/1
fffffbBbbbcccccfffffefffffffffeffffffffefffffdefffd
[srp101]


> s6<-readFastq("./", "tmp2")
> q6<-qa(s6)
Error: UserArgumentMismatch
  'lane' must be 'character(1)'


> sessionInfo()
R version 2.11.0 (2010-04-22) 
x86_64-unknown-linux-gnu 

locale:
 [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            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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


other attached packages:
[1] ShortRead_1.6.2     Rsamtools_1.0.1     lattice_0.18-8     
[4] Biostrings_2.16.7   GenomicRanges_1.0.1 IRanges_1.6.8      

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2  
>

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