[Useq-users] MultipleReplicaScanSeqs / ScanSeqs Problem

[Kathrin P. <kp...@un...>]

Hi David

thanks for the great applications provided by USeq.

I'am analyzing some CHIP-seq data using USeq and by running the
'MultipleReplicaScanSeqs' script I got some error messages, even by
using 'ScanSeqs' those messages appear :(
The functions cannot read-in the chrY_-_.bar.zip files from the control
data, I generated the point data files with 'Tag2Point'. By swapping the
treatment and the control directories the same error occurs.

Additionaly, I got a java.io.FileNotFoundException and an 'R has a
problem in estimating the binomial P values' error that might be
consequences of the former one!?!

Do you have an idea for solving my problem?

Thanks in advance
Kathrin

Code example:

kathrin@server:$ java -Xmx4G -jar <pathToUSeq>/Apps/ScanSeqs -t
<pathOfTreatment> -c <pathOfInput> -s <pathOfResults> -p 100 -w 250

Arguments: -t <pathOfTreatment> -c <pathOfInput> -s <pathOfResults> 
	   -p 100 -w 250

Scanning for enriched regions...
	2	Minium number reads in window
	100	Peak shift
	250	Window size
Calculating read count stats and binomial p-value look up tables...
	20449873	Treatment Observations
Cannot read <pathOfInput>/chrY_-_.bar.zip
java.util.zip.ZipException: error in opening zip file
	at java.util.zip.ZipFile.open(Native Method)
	at java.util.zip.ZipFile.<init>(ZipFile.java:131)
	at java.util.zip.ZipFile.<init>(ZipFile.java:148)
	at edu.utah.seq.parsers.BarParser.loadSimpleBarFile(BarParser.java:161)
	at edu.utah.seq.parsers.BarParser.readBarFile(BarParser.java:141)
	at edu.utah.seq.data.PointData.<init>(PointData.java:38)
	at
edu.utah.seq.data.PointData.fetchStrandedPointDataNoMerge(PointData.java:1277)
	at
edu.utah.seq.analysis.ScanSeqs.calculateReadCountStatistics(ScanSeqs.java:931)
	at edu.utah.seq.analysis.ScanSeqs.scan(ScanSeqs.java:119)
	at edu.utah.seq.analysis.ScanSeqs.<init>(ScanSeqs.java:107)
	at edu.utah.seq.analysis.ScanSeqs.main(ScanSeqs.java:1307)
	17026011	Control Observations
java.io.FileNotFoundException: <pathOfResults>/3C6G8Q_Scores.txt
(Operation not permitted)
	at java.io.FileOutputStream.open(Native Method)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:209)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:160)
	at java.io.FileWriter.<init>(FileWriter.java:90)
	at util.gen.Num.binomialPValues(Num.java:623)
	at util.gen.Num.binomialPValMatrix(Num.java:749)
	at
edu.utah.seq.analysis.ScanSeqs.calculateReadCountStatistics(ScanSeqs.java:947)
	at edu.utah.seq.analysis.ScanSeqs.scan(ScanSeqs.java:119)
	at edu.utah.seq.analysis.ScanSeqs.<init>(ScanSeqs.java:107)
	at edu.utah.seq.analysis.ScanSeqs.main(ScanSeqs.java:1307)

Problem with estimating binomial pvalues in R.


-- 
MSc Kathrin Poos        

Institute of Bioinformatics
Muenster University Medical Center
Niels-Stensen Str 12
48149 Muenster
Germany

Phone +49-251-83-50 004
Fax   +49-251-83-53 005
email kp...@un...
http://bioinformatics.uni-muenster.de/