Menu
▾
▴
Re: [Useq-users] help ( USeq - ChIPSeq Cannot find the required R libraries)
|
From: David A. N. <dav...@gm...> - 2014-08-21 21:51:34
|
Hello Ashutosh,
Sorry for the delay in responding… it’s been a crazy summer…. let’s see….
Hmm, have you tried explicitly setting which R to use? By default it is going to /usr/bin/R. So try using the -r flag. See the cmd menu.
-cheers, David
nix-laptop:~ u0028003$ java -jar -Xmx4G ~/AppsUSeq/ChIPSeq
**************************************************************************************
** ChIPSeq: May 2014 **
**************************************************************************************
The ChIPSeq application is a wrapper for processing ChIP-Seq data through a variety of
USeq applications. It:
1) Parses raw alignments (sam, eland, bed, or novoalign) into binary PointData
2) Filters PointData for duplicate alignments
3) Makes relative ReadCoverage tracks from the PointData (reads per million mapped)
4) Runs the PeakShiftFinder to estimate the peak shift and optimal window size
5) Runs the MultipleReplicaScanSeqs to window scan the genome generating enrichment
tracks using DESeq2's negative binomial pvalues and B&H's FDRs
6) Runs the EnrichedRegionMaker to identify likely chIP peaks (FDR < 1%, >2x).
Options:
-s Save directory, full path.
-t Treatment alignment file directories, full path, comma delimited, no spaces, one
for each biological replica. These should each contain one or more text
alignment files (gz/zip OK) for a particular replica. Alternatively, provide
one directory that contains multiple alignment file directories.
-c Control alignment file directories, ditto.
-y Type of alignments, either novoalign, sam, bed, or eland (sorted or export).
-v Genome version (e.g. H_sapiens_Feb_2009, M_musculus_Jul_2007), see UCSC FAQ,
http://genome.ucsc.edu/FAQ/FAQreleases.
-r Full path to R, defaults to '/usr/bin/R'. Be sure to install DESeq2, gplots, and
qvalue Bioconductor packages.
Advanced Options:
-m Combine any replicas and run single replica analysis (ScanSeqs), defaults to
using DESeq2.
-a Maximum alignment score. Defaults to 60, smaller numbers are more stringent.
-q Minimum mapping quality score. Defaults to 13, bigger numbers are more stringent.
This is a phred-scaled posterior probability that the mapping position of read
is incorrect. Set to 0 for RNASeq data.
-p Peak shift, defaults to the PeakShiftFinder peak shift or 150bp. Set to 0 for
RNASeq data.
-w Window size, defaults to the PeakShiftFinder peak shift + stnd dev or 250bp.
-i Minimum number reads in window, defaults to 10.
-f Filter bed file (tab delimited: chr start stop) to use in excluding intersecting
windows while making peaks, e.g. satelliteRepeats.bed .
-g Print verbose output from each application.
-e Don't look for reduced regions.
Example: java -Xmx2G -jar pathTo/USeq/Apps/ChIPSeq -y eland -v D_rerio_Dec_2008 -t
/Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/PolIINRep1/,/Data/PolIINRep2/ -s
/Data/Results/WtVsNull -f /Anno/satelliteRepeats.bed
**************************************************************************************
nix-laptop:~ u0028003$
On Jul 15, 2014, at 12:01 PM, Ashutosh Shukla <ash...@cc...> wrote:
> Dear All,
>
> I am trying to use USeq package for ChIP-Seq analysis. I have installed required packages DESeq2 , gplots and qvalue in a user local library ("~/R/x86_64-unknown-linux-gnu-library/3.1").
> When I open R in command line, i could see library(DESeq2),library(gplots) and library(qvalue) are present there. Now, when I try to run ChIPSeq using command
>
> $ java -Xmx2G -jar /home/pb/USeq_8.8.1/Apps/ChIPSeq -y novoalign -v S_cerevisiae_Apr_2011 -t /home/pb/Desktop/test/ -c /home/pb/Desktop/control/ -s /home/pb/Desktop/SAVE/
>
> I get the following error:
>
> Checking parameters...
>
> The following problems were encountered when processing your parameter file. Correct and restart. ->
>
> Error: Cannot find the required R libraries. Did you install DESeq2, gplots, and qvalue? Once installed, launch an R terminal and type 'library(DESeq2); library(qvalue); library(gplots)' to see if it is present. Error message:
> Error in library(DESeq2) : there is no package called ‘DESeq2’ Execution halted
>
> is this error because of ChIPSeq only works with global R library? but not with library in my local folders.
>
> -- to check this problem i even tried to install all the required packages and dependencies one after another in /usr/local/lib/R/site-library but i got the following error
>
> Checking parameters...
>
> The following problems were encountered when processing your parameter file. Correct and restart. ->
>
> Error: Cannot find the required R libraries. Did you install DESeq2, gplots, and qvalue? Once installed, launch an R terminal and type 'library(DESeq2); library(qvalue); library(gplots)' to see if it is present. Error message:
> Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/site-library/RcppArmadillo/libs/RcppArmadillo.so': libRlapack.so: cannot open shared object file: No such file or directory Error: package ‘RcppArmadillo’ could not be loaded Execution halted.
>
> am i doing something wrong with the commands and package installations ? I am basically a biologist who recently started learning Linux and R. so please bear me , if I am asking a trivial question. any elaborated help would by highly appreciated.
>
> Thanks for help
> --
> Ashutosh Shukla
> Senior Research Fellow
> W313, West wing, IInd floor,
> Centre For Cellular & Molecular Biology
> Hyderabad -500007
> India.
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> Useq-users mailing list
> Use...@li...
> https://lists.sourceforge.net/lists/listinfo/useq-users
|