Re: [Useq-users] MultipleReplicaScanSeqs / ScanSeqs Problem

[David N. <Dav...@hc...>]

Hello Kathrin,

Looks like that zip file is corrupted.  Try uncompressing it or testing the
archive with "unzip -t chrY_-_.bar.zip" .  If those fail then try rerunning
the Tag2Point.  

-cheers, D


-- 
David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer
Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc:
801.587.4611 | Fx: 801.585.6458 | dav...@hc... | Skype/iChat:
LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2:
http://bioserver.hci.utah.edu:8080/DAS2DB/genome



On 9/29/10 5:26 AM, "Kathrin Poos" <kp...@un...> wrote:

> 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.
>