Re: [Useq-users] USEQ : java.io.IOException: DESeq2 R results file doesn't exist.

[Jean-Philippe V. <jpv...@gm...>]

Hi,
Sorry for multiple receptions...



I met problems using USEQ for ChIPSeq.

  UPDATE : Maybe it's relative to that

https://support.bioconductor.org/p/83850/


Caused by latter version of DESeq2 so how I recompile all the executables ?


Could you give a hand on this ?

Thanks !

*Command : *

java -Xmx4G -jar /home/jean-philippe.villemin/bin/USeq_8.9.6/Apps/ChIPSeq
-y sam -v H_sapiens_Dec_2013 -t
/home/jean-philippe.villemin/data/data/USEQ/T1/K4ME1
-c /home/jean-philippe.villemin/data/data/USEQ/T1/INPUT -s
/home/jean-philippe.villemin/CHIPSEQ_2017_1_ALL/USEQ -r
/home/jean-philippe.villemin/bin/anaconda3/lib/R/bin/R

*In the output :*
*.... *
Calculating individual peak shifts for top 100...
90 Median peak shift
246 Mean peak shift
310.4 Stnd dev peak shifts

Could not robustly identify the peak shift in your data, using the default
150bp peak shift and 250bp window size.

************************************************************
*******************

Scanning chromosomes for differential enrichment/reduction with
MultipleReplicaScanSeqs...
Stats and parameters...
92704636 Treatment Observations
39079825 Control Observations
150 Peak shift
250 Window size
15 Minimum number reads in window
java.io.IOException:
DESeq2 R results file doesn't exist. Check temp files in save directory for
error.

at edu.utah.seq.analysis.MultipleReplicaScanSeqs.executeDESeq2(
MultipleReplicaScanSeqs.java:337)
at edu.utah.seq.analysis.MultipleReplicaScanSeqs.run(
MultipleReplicaScanSeqs.java:139)
at edu.utah.seq.analysis.MultipleReplicaScanSeqs.<init>
(MultipleReplicaScanSeqs.java:99)
at edu.utah.seq.analysis.ChIPSeq.scanSeqs(ChIPSeq.java:174)
at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:86)
at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:442)

*In tmp files , in RScript.txt.Rout : *

Warning message:
package ‘RColorBrewer’ was built under R version 3.3.2
> countTable = read.delim('/home/jean-philippe.villemin/mount_
archive2/commun.luco/EMT_2015_SEQ_data/EMT_CHIPSEQ_FILES/2017/Luco/USEQ/
MultipleReplicaScanSeqs/TempRDir_XQKXQ8D/matrixFile.txt', header=FALSE)
> rownames(countTable) = countTable[,1]
> countTable = countTable[,-1]
> sampleInfo = data.frame(condition=as.factor(c('T','C')))
> rownames(sampleInfo) = c('T0','C0')
> cds = DESeqDataSetFromMatrix(countData=countTable, colData=sampleInfo,
design = ~condition)
Error in FUN(X[[i]], ...) :
  assay colnames() must be NULL or equal colData rownames()
Calls: DESeqDataSetFromMatrix ... SummarizedExperiment ->
SummarizedExperiment -> .local -> vapply -> FUN
Execution halted

-- 
*Jean-Philippe Villemin   *- Bioinformatics, Software Engineer -

IGH (Institute of Human Genetics)

Team: Splicing and Epigenetics
141 rue de la Cardonille
Montpellier France 4094 cedex 5

*jpv...@gm... <jpv...@gm...>*