Re: [Useq-users] problem with MultipleReplicaScanSeqs

[David N. <dav...@gm...>]

Looks like DESeq isn't generating a results file (this is the analysis
engine for MRSS, SS uses something simpler).

Take a look at the temp files in your save directory.  One should contain
the error that R/DESeq threw.

-cheers, D


On 4/5/11 4:58 PM, "Noboru Jo Sakabe" <ns...@uc...> wrote:

> java -Xmx8G -jar 
> /cchome/nsakabe/chip-seq/useq/USeq_7.6.9/Apps/MultipleReplicaScanSeqs -c
> /cchome/nsakabe/chip-seq/useq/input.merged/useq_pointData_satellites_rmsk_Filt
> 0bp/ 
> -s results -p 100 -w 200 -r /apps/rh5_64/R -t
> ../h3k27me3.left_ventricle_1/useq_pointData_satellites_rmsk_Filt0bp/
> 
>     Hi David, I am trying to run MRSS, but I'm getting an error.
>     When I use the same command line, but instead of MRSS, calling
> ScanSeqs, it works fine. The problem seems to be with MRSS. Do you have
> any idea what might be going on?
> 
>     Thank you.
> 
> java -Xmx8G -jar ~/useq/USeq_7.6.9/Apps/MultipleReplicaScanSeqs -c
> ../input/useq_pointData_satellites_rmsk_Filt0bp/ -s results -p 100 -w
> 200 -r /apps/rh5_64/R -t ../h3k27me3/useq_pointData_satellites_rmsk_Filt0bp/
> 
> 
> 
> Arguments: -c ../input/useq_pointData_satellites_rmsk_Filt0bp/ -s
> results -p 100 -w 200 -r /apps/rh5_64/R -t
> ../h3k27me3/useq_pointData_satellites_rmsk_Filt0bp/
> 
> Calculating read count stats...
>     19985712 Treatment Observations
>     36594184 Control Observations
>     100    Peak shift
>     200    Window size
>     0.5    Minimum Window FDR
> Scanning chromosomes......................
> Calculating negative binomial p-values and FDRs in R using DESeq
> (http://www-huber.embl.de/users/anders/DESeq/). This requires patience,
> 64bit R, and > 6-8G RAM...
> java.io.IOException:
> R results file(s) doesn't exist. Check temp files in save directory for
> error.
> 
>     at 
> edu.utah.seq.analysis.MultipleReplicaScanSeqs.executeDESeq(MultipleReplicaScan
> Seqs.java:353)
>     at 
> edu.utah.seq.analysis.MultipleReplicaScanSeqs.run(MultipleReplicaScanSeqs.java
> :146)
>     at 
> edu.utah.seq.analysis.MultipleReplicaScanSeqs.<init>(MultipleReplicaScanSeqs.j
> ava:80)
>     at 
> edu.utah.seq.analysis.MultipleReplicaScanSeqs.main(MultipleReplicaScanSeqs.jav
> a:682)
> 
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