useq-users

[Useq-users] error in ScanSeqs

[Noboru Jo S. <nob...@gm...>]

    Hi David, I am getting this error from ScanSeqs. Do you know what 
it's about?

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
    at edu.utah.seq.data.PointData.combinePointData(PointData.java:1142)
    at edu.utah.seq.data.PointData.combinePointData(PointData.java:1129)
    at 
edu.utah.seq.analysis.ScanSeqs.subSamplePointDataForEmpFDR(ScanSeqs.java:670)
    at 
edu.utah.seq.analysis.ScanSeqs.calculateBinomialPValsForEmpiricalFDRs(ScanSeqs.java:568)
    at 
edu.utah.seq.analysis.ScanSeqs.windowScanChromosome(ScanSeqs.java:278)
    at edu.utah.seq.analysis.ScanSeqs.scan(ScanSeqs.java:126)
    at edu.utah.seq.analysis.ScanSeqs.<init>(ScanSeqs.java:107)
    at edu.utah.seq.analysis.ScanSeqs.main(ScanSeqs.java:1307)


    This is the command I'm issuing.
java -Xmx5500M -jar USeq_7.1.2/Apps/ScanSeqs -t 
treatment/useq_pointData_satellites_rmsk_Filt0bp/ -c 
control/useq_pointData_satellites_rmsk_Filt0bp/ -s ./results -p 100 -w 200

    I've never got this error before. It happened with a new input set. 
I was tempted to think that something went wrong when converting from 
.bed to Useq internal format, but Tag2Point seems to be reading 
coordinates correctly.
    .bed file is fine, as I was able to use it in other peak callers.

    FilterPointData also seems to be able to read the converted files.
Stats:
23452020    Starting
23040045    Ending
411975    Difference

    Any ideas what may be wrong?
    Thanks!

[Useq-users] error in ScanSeqs

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

    Hi David, I sent a message to the list from my other email, you can 
ignore it.
    I was getting this error from ScanSeqs, but I found the culprit. It 
seems that, sometimes, random chr cause this error. It may be because 
treatment/control don't have a random chr and ScanSeqs can't find the 
data to pair and crashes.


Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
   at edu.utah.seq.data.PointData.combinePointData(PointData.java:1142)
   at edu.utah.seq.data.PointData.combinePointData(PointData.java:1129)
   at 
edu.utah.seq.analysis.ScanSeqs.subSamplePointDataForEmpFDR(ScanSeqs.java:670) 

   at 
edu.utah.seq.analysis.ScanSeqs.calculateBinomialPValsForEmpiricalFDRs(ScanSeqs.java:568) 

   at 
edu.utah.seq.analysis.ScanSeqs.windowScanChromosome(ScanSeqs.java:278)
   at edu.utah.seq.analysis.ScanSeqs.scan(ScanSeqs.java:126)
   at edu.utah.seq.analysis.ScanSeqs.<init>(ScanSeqs.java:107)
   at edu.utah.seq.analysis.ScanSeqs.main(ScanSeqs.java:1307)