[Useq-users] problem with MultipleReplicaScanSeqs

[Noboru Jo S. <ns...@uc...>]

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_Filt0bp/ 
-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(MultipleReplicaScanSeqs.java:353)
    at 
edu.utah.seq.analysis.MultipleReplicaScanSeqs.run(MultipleReplicaScanSeqs.java:146)
    at 
edu.utah.seq.analysis.MultipleReplicaScanSeqs.<init>(MultipleReplicaScanSeqs.java:80)
    at 
edu.utah.seq.analysis.MultipleReplicaScanSeqs.main(MultipleReplicaScanSeqs.java:682)