Hi Martin Thanks for a quick reply. I understand the problem now. The export file I am using is 2 GB and that would definitely crash my system if the req are 3-5 times more. Right now I am trying at my dev machine. May be I should ask IT to install it centrally so that I can access it on a bigger machine.
For now let me I will pick a small chunk to do some initial tests. Thanks, _Abhi -----Original Message----- From: Martin Morgan [mailto:[email protected]] Sent: Friday, July 10, 2009 11:25 AM To: Pratap, Abhishek Cc: [email protected] Subject: Re: [Bioc-sig-seq] About ShortRead Package Hi Abhi -- Pratap, Abhishek wrote: > Hi All > > > > I have recently started to acquaint my self with new R packages for NGS > data processing/analysis. I think the community has done a great work > in developing these packages. I must say I am amazingly surprised to see > some of the capabilities. > > > > I have a quick comment. While playing with ShortRead package I am not > able to successfully load the export file even one for that matter. I am > using a single PC to do this . I belv it has It has sufficient memory > (4 GB) to handle one lane of data. I waited for 15-18 minutes before my > pc started to show sign of sickness. I eventually had to kill the > process. > > > > Here is wat I did. > > > > Library(ShortRead) > > sp=SolexaPath("/local/seq_archive/solexa/090309_HWI-EAS397_0006") > > path=analysisPath(sp)[4] ### I just wanted to look at one GERALD > folder. > > aln=readAligned(path,type="SolexaExport","s_6_export.txt") One tricky point is the number of files specified by your pattern. Does list.files(path, "s_6_export.txt") return just a single file? if not (e.g., because there are both .txt and .txt.gz versions of s_6_export) then specify the pattern more precisely, e.g., "^s_6_export.txt$" It might be that your computer does not have enough memory. Very roughly, for this initial stage, you might expect R to require 3-5 times as much memory as the file occupies on disk. If your reads are relatively short, your files might be 500MB or so and you might be fine, but if your reads are longer the files could be > 1GB and you'd be in trouble. There are several options, the best being to use a computer with more memory. You could also split the export file (using unix 'split' command, for instance). We have also been working on making input more space- and time- efficient, so the version of ShortRead available with the development version of R will do a better job (but still require considerable memory). Martin > GOT STUCK HERE > > > > Is there anything I am doing the wrong way. Please let me know. > > > > Cheers, > > -Abhi > > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences <http://www.igs.umaryland.edu/> > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > > > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
