Hi  Martin

 

I am noticing a lethargic or may be hanged processing with qa()
function in ShortRead. I know I have raised this question before.
Recently I have updated my R to dev version and installed latest
bioconductor.Currently I am trying to run qa()  on 8 lanes of data for
75 bp reads.  The CPU is 16 cores with 16 GB RAM.

 

It has been two hours since the processing has been going on. Is it
usually takes so long. I am not sure.  Will using Rmpi help ?

 

 

Thanks,

-Abhi

 

sessionInfo()

R version 2.9.2 (2009-08-24) 

x86_64-unknown-linux-gnu 

 

locale:

LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
ON=C

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base


 

other attached packages:

[1] ShortRead_1.2.1   lattice_0.17-25   BSgenome_1.12.3
Biostrings_2.12.8

[5] IRanges_1.2.3    

 

loaded via a namespace (and not attached):

[1] Biobase_2.4.1 grid_2.9.2    hwriter_1.1  

 

 


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