Hi Peter,
Thanks for the reply.
I checked the history view. I don't see anything when I clicked the "i"
icon and click the stderr link. However, here is what I see if I click the
little bug icon next to the "i":
Tool execution generated the following error message:
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval,
Filter, Find, get, intersect, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist
Loading required package: IRanges
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: Rcpp
Loading required package: RcppArmadillo
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting generalized linear model
All these are the normal output message from loading the 'Deseq2' package
in R, and run some functions. After I use
suppressMessages(Library("DESeq2"))
to suppress the library loading messages, now, the following lines appear
if I click "i" and then click "stderr"
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting generalized linear model
I guess I need to suppress them as well -- but how come they are on stderr
not stdout?
Thanks,
Rui
On Sun, Sep 29, 2013 at 3:36 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:
> On Sun, Sep 29, 2013 at 8:47 PM, ruiwang.sz <ruiwang...@gmail.com> wrote:
> > Hi Guys,
> >
> > I'm doing a very simple test about deseq2...there is a weird situation
> > always happening:
> >
> > It looks like the deseq2 tool executed just fine, without any error, and
> the
> > result files were created, but after the set_metadata, galaxy always 'set
> > dataset state to ERROR'.
> >
> > The xml file for this test is:
> >
> > <tool id="deseq2 test" name="DESeq2" version="2">
> > <description>Determines differentially expressed transcripts from read
> > alignments</description>
> > <command>
> > t.sh $input1 $test $out $log
> > </command>
> > <inputs>
> > <param format="txt" name="input1" type="data" label="Quant"/>
> > <param format="txt" name="input2" type="data" label="Conditions"/>
> > <param name="test" type="select" label="please choose control
> > condition">
> > <options from_dataset="input2">
> > <column name="value" index="0"/>
> > </options>
> > </param>
> > </inputs>
> >
> > <outputs>
> > <data format="txt" name="out" label="DESeq result"/>
> > <data format="txt" name="log" label="DESeq log file"/>
> > </outputs>
> > </tool>
> >
> > Basically, we have an input file from Partek flow(input1), input2 is one
> > column
> > from input1, which has all the conditions, in our test, it has 3
> conditions,
> > CTC, LM, PT.
> >
> > input name "test" is the dropdown list that contain all 3 conditions,
> and we
> > choose
> > one as control condition, in our case it is CTC.
> >
> > t.sh is very simple, it basically calls R script:
> >
> > Rscript /home/bioinfo/app/galaxy-dist/tools/Deseq/workflow.R $1 $2 $3 $4
> >
> > now, in the workflow.R, the related output part is:
> >
> > for (i in 2:3) {
> > res <- results(dds, contrasts[i])
> >
> > ## sort the result table by FDR
> > res <- res[order(res$padj),]
> >
> > ## Output the results
> > write.table(as.data.frame(res), file=paste0(args[i+1]), sep = "\t")
> > }
> >
> > So, it looks like the result files were generated as expected, with the
> > correct information.
> > However, it always was set to state ERROR. Am I missing something? Or did
> > anyone see this before?
> >
> > Any inputs will be greatly appreciated!
> >
> > Thanks,
> > Rui
>
> Hi Rui,
>
> Was anything written to stderr, like a warning from R itself?
> You should be able to check via the "i" icon of the dataset
> in the history view.
>
> By default, Galaxy treats any output on stderr as an error,
> see the <stdio> tag information here:
> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>
> Peter
>
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