Mercurial > repos > lecorguille > probmetab
changeset 0:71047cbb3e6c draft default tip
planemo upload commit 858f2560108824c0c4d6e9f700d1690308bb13ad
| author | lecorguille |
|---|---|
| date | Tue, 24 May 2016 11:17:59 -0400 |
| parents | |
| children | |
| files | ProbMetab.xml README.txt export.class.table-color-graph.R lib.r nohup.out planemo_test.sh probmetab.r static/images/probmetab_workflow.png test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata |
| diffstat | 9 files changed, 3019 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProbMetab.xml Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,428 @@ +<tool id="Probmetab" name="ProbMetab Tool" version="1.0.1"> + + <description>Wrapper function for ProbMetab R package.</description> + + <requirements> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.0">r-probmetab</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command> + LANG=C Rscript $__tool_directory__/probmetab.r + #if $acquisition_options.mode == "one": + mode_acquisition $acquisition_options.mode xa $acquisition_options.xa + ##if $acquisition_options.xsetnofill_options.option == "show": + ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill + ##end if + #else + mode_acquisition $acquisition_options.mode inputs_mode $acquisition_options.input_mode.option + #if $acquisition_options.input_mode.option== "two": + + image_pos $acquisition_options.input_mode.image_pos image_neg $acquisition_options.input_mode.image_neg + ##if $acquisition_options.input_mode.xsetnofill_options.option == "show": + ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill + ##end if + ##else + ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos image_pos $acquisition_options.input_mode.image_pos + #end if + + #end if + + #if $option_toexclude.option == "show": + toexclude $option_toexclude.toexclude + #end if + allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol + opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob + + </command> + + <inputs> + + <conditional name="acquisition_options"> + <param name="mode" type="select" label="Choose your acquisition mode" > + <option value="one" selected="true" >One acquisition charge mode</option> + <option value="two" >Two acquisition charge mode (positif and negatif)</option> + </param> + + <!-- One acquisition mode--> + <when value="one"> + <param name="xa" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " /> + <!-- + <conditional name="xsetnofill_options"> + <param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" /> + </when> + + </conditional> + --> + </when> + <!-- Two acquisition modes--> + <when value="two"> + + + <conditional name="input_mode"> + <param name="option" type="select" label="Choose your input type method:" > + <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> --> + <option value="two" selected="true">Rdata inputs from annotate</option> + </param> + <!-- + <when value="one"> + <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " /> + <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " /> + </when> + --> + <when value="two"> + <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " /> + <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" /> + <!-- + <conditional name="xsetnofill_options"> + <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" /> + <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" /> + </when> + </conditional> + --> + </when> + </conditional> + </when> + + </conditional> + + + <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." /> + <conditional name="option_toexclude"> + <param name="option" type="select" label="Exclude samples" > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" /> + </when> + <when value="hide" /> + </conditional> + <!-- + <conditional name="useIso_options"> + <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" > + <option value="show">Yes</option> + <option value="hide" selected="true">No</option> + </param> + <when value="show"> + <param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." > + <option value="1">1</option> + <option value="2" selected="true">2</option> + </param> + </when> + </conditional> + --> + <param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help=" [html] (export.class.table function).This parameter uses the raw data to plot EICs and may be time consuming." /> + + <param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" > + <validator type="empty_field"/> + </param> + <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol] (create.reactionMfunction) " /> + + + <param name="opt" type="select" label="Correlation option" help="[opt] (reac2cor function) cor for correlation, and pcor for partial correlation." > + <option value="cor" selected="true">cor</option> + <option value="pcor">pcor</option> + </param> + + + <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " /> + + + <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob](reac2cor function)" /> + <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths] (reac2cor function)" /> + + <param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] (export.class.table function). Default is 'count'. See the tool help for more details." > + <option value="count" selected="true">Count</option> + <option value="mean">Mean</option> + </param> + <!-- + <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms). +" /> + + --> + + </inputs> + + <outputs> + <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> --> + <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" > + <filter>(html)</filter> + </data> + <data name="tsv_output" format="tabular" from_work_dir="Analysis_Report.tsv" label="Probmetab.CytoScape_output_Attribute_List.tsv" /> + <data name="eics" format="zip" from_work_dir="Analysis_Report.zip" label="Probmetab.Analysis_Report_EICs_plots.zip" > + <filter>(html)</filter> + </data> + <data name="sif_output" format="tabular" from_work_dir="sif.tsv" label="Probmetab.CytoScape_output.sif" /> + <data name="log" format="txt" from_work_dir="probmetab.log" label="Probmetab.log" /> + <data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" > + <filter>(acquisition_options['mode'] == 'one')</filter> + </data> + + <data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" > + <filter>(acquisition_options['mode'] == 'two')</filter> + </data> + <data name="variableMetadata_Positive" format="tabular" from_work_dir="variableMetadata_Positive.tsv" label="variableMetadata_Positive.tsv" > + <filter>(acquisition_options['mode'] == 'two')</filter> + </data> + <data name="variableMetadata_Negative" format="tabular" from_work_dir="variableMetadata_Negative.tsv" label="variableMetadata_Negative.tsv" > + <filter>(acquisition_options['mode'] == 'two')</filter> + </data> + + </outputs> + + <tests> + <test> + <param name="acquisition_options|mode" value="one" /> + <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> + <output name="log"> + <assert_contents> + <has_text text="ko15 ko16 wt15 wt16" /> + <has_text text="Step 1... determine cutoff point" /> + <has_text text="Step 2... estimate parameters of null distribution and eta0" /> + <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" /> + <has_text text="Step 4... compute q-values and local fdr" /> + </assert_contents> + </output> + + + + + + + + DONE + </test> + </tests> + + + <help> + +.. class:: infomark + +**Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br + + | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics.. + | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/ + +.. class:: infomark + +**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +.. class:: infomark + +**Contributors** Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr + +--------------------------------------------------- + + +========= +ProbMetab +========= + +----------- +Description +----------- + +**What it does?** + +ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography-mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions. + + +**Details** + +ProbMetab assumes peak detection, retention time correction and peak grouping [4, 5] in order to +perform mass peak to compound assignment. + +Once the initial annotation for different forms of the same ion (adducts and isotopes), is defined, +one can seek for a non-redundant set of putative molecules (after charge and possible adduct +correction) for further inference of compound identity. + +Experience shows that standard mass rules for adduct search may lose peaks, and specific rule tables must be setup for a given +experimental condition. In order to address this issue, a flexible workflow, which allows users to +integrate different methods, would improve true molecular ions recovery. + +The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data. + + + + +----------------- +Workflow position +----------------- + + +**Upstream tools** + +========================= ========================================== ======= ========== +Name Output file Format Parameter +========================= ========================================== ======= ========== +xcms.annotate xset.annotate_POS (or NEG).RData RData RData file +========================= ========================================== ======= ========== + + +**General schema of the metabolomic workflow** + +.. image:: probmetab_workflow.png + + +----------- +Input files +----------- + ++---------------------------+------------+ +| Parameter : label | Format | ++===========================+============+ +|RData Input | RData | ++---------------------------+------------+ +|RData group step | RData | ++---------------------------+------------+ + + +---------- +Parameters +---------- + +**Allow Miss** + + +Optionally retrieves peaks with no evidence of adduct or isotope and annotate them as single charged molecules [M+/-H]. + + +**polarity** + + +Acquisition mode of mass spectrometer. + + +**Exclude samples** + + +Samples to be excluded of peak counting to non-annotated peak selection. + +**Calculate** + +**intervals** +A vector of SNR numerical intervals, to which different carbon offset should be added to predicted C-number. + +**offset** + +A vector of empirically estimated carbon offset to be added to predicted C-number. + +**massWeigth** +Is the contribution parameter of the probabilistic model. + +**likelihood** + +Which noise model to use, "erfc" to complementary error function, or "gaussian" to standard gaussian with two sd corresponding to the given p.p.m precision. + +**precision** + +Equipment mass accuracy, usually the same used in exact mass search. + +**KEGG database** + + +Select if you want to search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at "http://rest.kegg.jp/list/organism". + +**ppm.tol** + + +Parts per million mass tolerance allowed in the mass search (create.reactionMfunction). + +**HTML** + + +Logical, check if you want to generate a HTML ProbMetab report.This parameter uses the raw data to plot EICs and may be time consuming. + +**opt** + + +(reac2cor function) Correlation option, cor for correlation, and pcor for partial correlation. + +**corprob** + +(reac2cor function) Probability that the correlation is considered significant. + + +**pcorprob** + + +(reac2cor function) Probability that the partial correlation is considered significant. + +**corths** + + +(reac2cor function) Correlation intensity threshold. + +**prob** + +(export.class.table). How to calculate the probability to attribute a mass to a compound. Default is "count", which divide the number of times each identity was was attributed by the number of samples. Optionally the user could choose to use the mean of the probabilities of the identity, "mean". + + +**organismIdorganismId** + +(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possibibly pathwyas for known pathways for that organism. Only works for KEGG database for now. Default isNULL (all KEGG organisms). + + + +------------ +Output files +------------ + +Probmetab.RData + | Rdata file, that be used outside Galaxy in R. + +Probmetab.Analysis_Report_htmlSelect if you want to search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism + | A list with a matrix "classTable" with attributions and probabilities and indexes of selected masses from xcms peak table (HTML format). + +Probmetab.CytoScape_output_Attribute_List.tsv + | A list with a matrix "classTable" with attributions and probabilities and indexes of selected masses from xcms peak table, that can be used as Attribute table list in CytoScape (tsv format). + +Probmetab.Analysis_Report_EICs_plots + | Zip file containing the EIC plots (PNG format) of the metabolites that are listed in the HTML or tsv report. + +Probmetab.CytoScape_output.sif + | Sif format file that can be used in CytoScape to visualize the network. + + +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 1.0.1 - 16/05/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + +**Version 1.0.0 - 10/06/2015** + +- NEW: ProbMetab first version + + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu019</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> +</tool> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,19 @@ +Changelog/News +-------------- + +**Version 1.0.1 - 16/05/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + +**Version 1.0.0 - 10/06/2015** + +- NEW: ProbMetab first version + + +Test Status +----------- + +Planemo test using conda: passed + +Planemo shed_test : passed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/export.class.table-color-graph.R Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,455 @@ +#' export.class.table +#' +#' Builds a matrix with the probability for all mass to candidate compounds +#' assignments, by averaging the number of assignments obtained by the gibbs sampler algorithm +#' or ordering the compound candidates with the likelihood matrix. +#' +#' @param gibbsL a list of attributions and probabilities from gibbs.samp function. +#' @param reactionM data.frame with compound annotation information. +#' @param molIon non redundant ion annotation. +#' @param probM optionally to gibbsL, a matrix of likelihoods. +#' @param html logical, indicating whether a html file should be generated. This parameter uses the raw data to plot EICs and may be time consuming. +#' @param filename html file name, the default is "test". +#' @param burnIn how many samples of the gibbs sampler should be discarded. +#' @param linkPattern which pattern should be linked to compound id, for now we have +#' implemented "kegg", "pubchem" and "chebi" patterns. +#' @param m.test statistical test to compare mean differences. This option +#' is only available to single acquisition mode analysis, with options +#' "t.test" and "anova". +#' @param class1 if the m.test is "t.test" first class to compare in the test, +#' according with xcmsSet phenoData. +#' @param class2 if the m.test is "t.test" second class to compare in the test, +#' according with xcmsSet phenoData. +#' @param norm logical, if TRUE performs median normalization from (Anal. Chem. 2011, 83, 5864-5872). +#' @param DB data.frame table used to search compounds, with the field name to be incorporated in the html table. +#' @param prob how to calculate the probability to attribute a mass to a compound. +#' Default is "count", which divide the number of times each identity was +#' was attributed by the number of samples. Optionally the user could +#' choose to use the mean of the probabilities of the identity, "mean". +#' @return A list with a matrix "classTable" with attributions and probabilities and +#' indexes of selected masses from xcms peak table. +#' +#' @export + +export.class.table <- function(gibbsL=NULL, reactionM, molIon=NULL, probM=NULL, html=FALSE, filename="test", burnIn=3000, linkPattern="kegg", m.test="none", class1=NULL, class2=NULL, norm=FALSE, DB, prob="count", colorplot=FALSE, addLink=NULL) { + + plotEIC <- function (xcmsObject, figidx, pngidx, colorplot, mode=NULL) { + dir.create(paste(filename,"_fig",sep="")) + gt<-groups(xcmsObject) + if(colorplot==TRUE){ + gt2 <- gt[figidx,] + rgt <- gt2[,c("rtmin","rtmax")] + rgt[,1] <- rgt[,1]-100 + rgt[,2] <- rgt[,2]+100 + #require(doMC) + #registerDoMC() + #system.time( + #foreach(i=1:nrow(gt2)) %dopar% { + for(i in 1:nrow(gt2)){ + groupidx1 <- which(gt[,"rtmed"] > rgt[i,1] & gt[,"rtmed"] < rgt[i,2] & gt[,"mzmed"]> gt2[i,"mzmed"]-0.1 & gt[,"mzmed"]< gt2[i,"mzmed"]+0.1) + eiccor <- getEIC(xcmsObject, groupidx = groupidx1) + png(paste(filename, "_fig/", sprintf("%003d", i), ".png", sep="")) + plot(eiccor, xcmsObject, groupidx = 1) + dev.off() + } + } else { + gt <- gt[figidx,] + rgt <- gt[,c("rtmin","rtmax")] + rgt[,1] <- rgt[,1]-100 + rgt[,2] <- rgt[,2]+100 + + eics <- getEIC(xcmsObject, mzrange=gt, rtrange =rgt, groupidx = 1:nrow(gt)) + png(file.path(paste(filename, "_fig/%003d.png", sep="")), height=768, width=1024) + #png(file.path(paste(filename, "_fig/", pngidx, sep="")), h=768, w=1024) + plot(eics, xcmsObject) + dev.off() + } + if(!is.null(mode)) { + pngs <- dir(paste(filename, "_fig/", sep="")) + if(length(grep("pos|neg" , pngs))) pngs <- pngs[-grep("pos|neg" , pngs)] + opng <- as.numeric(sub(".png","", pngs)) + pngs <- pngs[order(opng)] + name1 <- paste(filename, "_fig/",pngs, sep="") + name2 <- paste(filename, "_fig/",pngidx, mode, ".png", sep="") + for(i in 1:length(name1)) file.rename(name1[i], name2[i]) + } + + } + allion <- molIon$molIon[molIon$molIon[,"isotope"]==0,] + ReactMatrix <- reactionM[reactionM[,5]!="unknown",] + x <- apply(unique(ReactMatrix[,c(2, 3)]), 2, as.numeric) # Have to look for all pairs + y <- as.numeric(ReactMatrix[,4]) + prob_mean_ma <- matrix(0, nrow = length(y), ncol = nrow(x)) +# z_average <- matrix(0, nrow = length(y), ncol = length(x)) + + if (!is.null(gibbsL)){ + prob_table <- gibbsL$prob_table[,-c(1:burnIn)] + class_table <- gibbsL$class_table[,-c(1:burnIn)] + #indList <- tapply(1:nrow(ReactMatrix), as.numeric(ReactMatrix[,1]), function(x) x) + coords <- tapply(1:nrow(ReactMatrix), ReactMatrix[,"molIonID"], function(x) x) + coords2 <- unlist(lapply(coords, function(x) rep(x[1], length(x)))) + indList <- coords[order(unique(coords2))] + fillMatrix <- function(j,i) { + idp <- which(class_table[i,] == j) + if(prob=="count") prob_mean_ma[j,i] <<- length(idp)/ncol(class_table) + if(prob=="mean") prob_mean_ma[j,i] <<- mean(prob_table[i,idp]) + } + + + for ( i in 1:nrow(x) ) { + + sapply(indList[[i]], fillMatrix, i) + } + if(sum(prob_mean_ma=="NaN")) prob_mean_ma[prob_mean_ma=="NaN"] <- 0 +# for ( i in 1:nrow(x) ) { +# for ( j in 1:length(y) ) { +# idp <- which(class_table[i,] == j) +# prob_mean_ma[j,i] <- mean(prob_table[i,idp]) +# # this is an alternative way to calculate the probabilities, should try latter, and compare results +# #prob_mean_ma[j,i] <- length(idp)/ncol(class_table) +# if ( prob_mean_ma[j,i] == "NaN" ) prob_mean_ma[j,i] <- 0 +# } +# # do I still need this matrix? +# k=which(prob_mean_ma[,i]==max(prob_mean_ma[,i])) +# z_average[k[1],i]=1 +# } + } + else { + prob_mean_ma <- probM + } + # think about natural probabilities + # prob_mean_ma[prob_mean_ma[,1]!=0,1]/sum(prob_mean_ma[prob_mean_ma[,1]!=0,1]) + prob_mean_ma <- apply(prob_mean_ma, 2, function(x){ x[x!=0] <- x[x!=0]/sum(x[x!=0]); return(x)} ) + + # create a dir to figures + lpattern <- function(type){ + switch(type, + kegg = "http://www.genome.jp/dbget-bin/www_bget?", + chebi = "http://www.ebi.ac.uk/chebi/searchId.do;EFB7DFF9E88306BBCD6AB78B32664A85?chebiId=", + pubchem = "http://www.ncbi.nlm.nih.gov/pccompound/?term=" + ) + } + linkURL <- lpattern(linkPattern) + fig <- paste("file://", getwd(), paste("/",filename,"_fig/",sep=""), sep="") + if(!is.null(molIon$cameraobj)) { + figidx <- c("") + coords <- gsub("(^\\d)","X\\1",rownames(molIon$cameraobj@xcmsSet@phenoData)) + # experimental! Which set of characters???? + coords <- gsub("-|\\,|~","\\.",coords) + coords <- gsub("\\s+","\\.",coords) + peaklist <- getPeaklist(molIon$cameraobj) + rpeaklist <- peaklist[,c("mz","rt","isotopes","adduct","pcgroup")] + } + else { + figidx <- c("","") + coordsP <- gsub("(^\\d)","X\\1",rownames(molIon$pos@xcmsSet@phenoData)) + # experimental! Which set of characters???? + coordsP <- gsub("-|\\,|~","\\.",coordsP) + coordsP <- gsub("\\s+","\\.",coordsP) + coordsN <- gsub("(^\\d)","X\\1",rownames(molIon$neg@xcmsSet@phenoData)) + # experimental! Which set of characters???? + coordsN <- gsub("-|\\,|~","\\.",coordsN) + coordsN <- gsub("\\s+","\\.",coordsN) + coords <- coordsP + if(length(coordsP)!=length(coordsN)) cat("\n Warning: The number of samples are different\n") + + peaklistP <- getPeaklist(molIon$pos) + rpeaklistP <- peaklistP[,c("mz","rt","isotopes","adduct","pcgroup")] + peaklistN <- getPeaklist(molIon$neg) + rpeaklistN <- peaklistN[,c("mz","rt","isotopes","adduct","pcgroup")] + } + +# if(sum(is.na(peaklist))) { +# cat("\nWarning: NAs Found in peaklist\n\nSubstituting for \"ones\"\n") +# na.ids <- which(is.na(peaklist),arr.ind=TRUE) +# for(l in 1:nrow(na.ids)){ +# peaklist[na.ids[l,][1], na.ids[l,][2]] <- 1 +# } +# } +# + + ans <- matrix("", nrow=1, ncol=7+length(coords)) + unq <- unique(ReactMatrix[,2:3]) + for (i in 1:nrow(unq)) { + coord <- which(ReactMatrix[,2]==unq[i,1] & ReactMatrix[,3]==unq[i,2]) + coord2 <- which(allion[,2]==unq[i,1] & allion[,1]==unq[i,2]) + # idx2 <- unique(which(allion[,1] %in% reactionM[reactionM[,5]=="unknown",2])) + # work with the higher intensities for a given ion annotation, not necessarily the right one + + if(!is.null(molIon$cameraobj)) { + idx <- as.vector(unlist(sapply(allion[coord2,"trace"], + function(x) { + x <- as.matrix(x) + raw <- strsplit(x,";")[[1]] + mraw <- apply(peaklist[raw, coords], 1, mean) + raw[which.max(mraw)] + } + + ) + ) + ) + + idx <- unique(idx) + figidx <- append(figidx,idx) + } + else { + idx <- c() + + for(l in 1:nrow( allion[coord2,c("trace","comb")])) { + x <- as.matrix(allion[coord2,c("trace","comb")][l,]) + raw <- strsplit(x[1],";")[[1]] + if(x[2]!="neg"){ + mraw <- apply(peaklistP[raw, coordsP], 1, mean, na.rm=TRUE) + } + else { + + mraw <- apply(peaklistN[raw, coordsN], 1, mean, na.rm=TRUE) + } + idx <- c(idx, raw[which.max(mraw)]) + } + + + idx <- unique(idx) + figidx <- rbind(figidx,c(idx,allion[coord2,"comb"][1])) + } + #figidx <- append(figidx,strsplit(allion[coord2,5], ";")[[1]][1]) + ans1 <- matrix("", nrow=length(coord), ncol=7+length(coords)) + ans1[,2]<-as.matrix(ReactMatrix[coord,5]) + prob <- as.matrix(prob_mean_ma[coord, i]) # need to change and compare a pair of mass/rt + # number figs + if ( i >= 100 ) { ans1[1,6]=i } + else { if ( i >= 10 ) { ans1[1,6]=paste(0,i, sep="") } else { ans1[1,6]=paste("00",i, sep="") } } + + if (sum(prob)>0) { + #prob <- prob/sum(prob) + o <- order(prob, decreasing=TRUE) + ans1[,-6] <- ans1[o,-6] + ans1 <- matrix(ans1, nrow=length(o)) + ans1[1,1] <- ReactMatrix[coord[1],3] + #ans1[,3] <- round(prob/min(prob[prob!=0]), 3)[o] + ans1[,3] <- round(prob, 3)[o] + if (length(prob[prob!=0])>1) { + entropy <- -sum(prob[prob!=0]*log(prob[prob!=0], length(prob[prob!=0]))) + } + else { entropy <- 0 + } + ans1[1,4] <- round(entropy, 3) + } + else { + ans1[1,1] <- ReactMatrix[coord[1],3] + ans1[1,3] <- "undef" + } + + if(!is.null(molIon$cameraobj)) { + ans1[1,7] <- apply(rpeaklist[idx,], 1, function(x) paste(x[c(1,2,3,4)], collapse="#")) + ans1[1,8:ncol(ans1)] <- as.matrix(peaklist[idx, coords]) + } + else { + if(allion[coord2,"comb"]=="pos"|allion[coord2,"comb"]=="both") { + ans1[1,7] <- apply(rpeaklistP[idx,], 1, function(x) paste(x[c(1,2,3,4)], collapse="#")) + ans1[1,8:ncol(ans1)] <- as.matrix(peaklistP[idx, coordsP]) + } + else { + ans1[1,7] <- apply(rpeaklistN[idx,], 1, function(x) paste(x[c(1,2,3,4)], collapse="#")) + ans1[1,8:ncol(ans1)] <- as.matrix(peaklistN[idx, coordsN]) + } + } + ans <- rbind(ans, as.matrix(ans1)) + } + ans <- ans[-1,] + # this option should change according with the bank + if(html) { + nid <- unlist(sapply(ans[,2], function(x) which(DB$id==x))) + #ans[,2] <- as.character(DB$name[nid]) + } + unk <- reactionM[reactionM[,5]=="unknown",] + ans1 <- matrix("", nrow=nrow(unk), ncol=7+length(coords)) + ans1[,1] <- unk[,3] + ans1[,2] <- unk[,5] + for(j in 1:nrow(ans1)) { + i <- j + max(as.numeric(ans[,6]),na.rm=TRUE) + if ( i >= 100 ) { ans1[j,6]=i } + else { if ( i >= 10 ) { ans1[j,6]=paste(0,i, sep="") } else { ans1[j,6]=paste("00",i, sep="") } } + } + # this step try to recover ids of ion annotation for masses without database annotation + idx2 <- c(); #for(m in 1:nrow(allion)) if(sum(allion[m,2]==as.numeric(unk[,2])) & sum(allion[m,1]==as.numeric(unk[,3]))) idx2 <- append(idx2, m) + # temp changes made 03/03/2014 have to check carefuly + lidx <- lapply(1:nrow(allion), function(m) which(allion[m,2]==unk[,2] & allion[m,1]==unk[,3])) + idx2 <- which(lapply(lidx, length)>0) + + if(!is.null(molIon$cameraobj)) { + idx <- as.vector(unlist(sapply(allion[idx2,"trace"], + function(x) { + x <- as.matrix(x) + raw <- strsplit(x,";")[[1]] + mraw <- apply(peaklist[raw, coords], 1, mean) + raw[which.max(mraw)] + } + + ) + ) + ) + } + + else { + # don't know what happened here with apply + idx <- c() + + for(i in 1:nrow( allion[idx2,c("trace","comb")])) { + x <- as.matrix(allion[idx2,c("trace","comb")][i,]) + raw <- strsplit(x[1],";")[[1]] + if(x[2]!="neg"){ + mraw <- apply(peaklistP[raw, coordsP], 1, mean, na.rm=TRUE) + } + else { + + mraw <- apply(peaklistN[raw, coordsN], 1, mean, na.rm=TRUE) + } + idx <- c(idx, raw[which.max(mraw)]) + } + + + + tmpidx <- cbind(idx,allion[idx2,"comb"]) + } + if(!is.null(molIon$cameraobj)) { + ans1[,7] <- apply(rpeaklist[idx,], 1, function(x) paste(x[c(1,2,3,4)], collapse="#")) + ans1[,8:ncol(ans1)] <- as.matrix(peaklist[idx, coords]) + } + else { + idxP <- tmpidx[tmpidx[,2]!="neg",1] + ans1[1:length(idxP),7] <- apply(rpeaklistP[idxP,], 1, function(x) paste(x[c(1,2,3,4)], collapse="#")) + ans1[1:length(idxP),8:ncol(ans1)] <- as.matrix(peaklistP[idxP, coordsP]) + idxN <- tmpidx[tmpidx[,2]=="neg",1] + ans1[(length(idxP)+1):nrow(ans1),7] <- apply(rpeaklistN[idxN,], 1, function(x) paste(x[c(1,2,3,4)], collapse="#")) + ans1[(length(idxP)+1):nrow(ans1),8:ncol(ans1)] <- as.matrix(peaklistN[idxN, coordsN]) + } + ans <- rbind(ans, as.matrix(ans1)) + + if(!is.null(molIon$cameraobj)) { + figidx <- c(figidx,idx) + figidx <- as.numeric(figidx[-1]) + } + else { + figidx <- rbind(figidx,tmpidx) + allidx <- figidx[-1,] + allidx <- cbind(allidx, ans[ans[,6]!="",6]) + figidx <- as.numeric(figidx[-1,1]) + } + + + if(m.test=="none") { + testname <- "none" + #testname <- "Formula" + #ans[ans[,2]!="unknown",][,5] <- as.character(DB$formula[nid]) + } + if(m.test=="t.test") { + normalize.medFC <- function(mat) { + # Perform median fold change normalisation + # X - data set [Variables & Samples] + medSam <- apply(mat, 1, median) + medSam[which(medSam==0)] <- 0.0001 + mat <- apply(mat, 2, function(mat, medSam){ + medFDiSmpl <- mat/medSam + vec<-mat/median(medFDiSmpl) + return(vec) + }, medSam) + return (mat) + } + # this piece of code was copied from xcms + pval <- function(X, classlabel, teststat) { + + n1 <- rowSums(!is.na(X[,classlabel == 0])) + n2 <- rowSums(!is.na(X[,classlabel == 1])) + A <- apply(X[,classlabel == 0], 1, sd, na.rm=TRUE)^2/n1 ## sd(t(X[,classlabel == 0]), na.rm = TRUE)^2/n1 + B <- apply(X[,classlabel == 1], 1, sd, na.rm=TRUE)^2/n2 ## sd(t(X[,classlabel == 1]), na.rm = TRUE)^2/n2 + df <- (A+B)^2/(A^2/(n1-1)+B^2/(n2-1)) + + pvalue <- 2 * (1 - pt(abs(teststat), df)) + invisible(pvalue) + } + + c1 <- grep(class1, molIon$cameraobj@xcmsSet@phenoData[,1]) + c2 <- grep(class2, molIon$cameraobj@xcmsSet@phenoData[,1]) + testclab <- c(rep(0, length(c1)), rep(1, length(c2))) + testval <- groupval(molIon$cameraobj@xcmsSet, "medret", "into") + if(norm) testval <- normalize.medFC(testval) + tstat <- mt.teststat(testval, testclab) + pvalue <- pval(testval, testclab, tstat) + +# +# rport <- diffreport(molIon$cameraobj@xcmsSet, class1=class1, class2= class2, sortpval=FALSE) +# ans[ans[,6]!="",5] <- rport[figidx, "pvalue"] + ans[ans[,6]!="",5] <- pvalue[figidx] + testname <- "t.test p-value" + } + if(m.test=="anova"){ + class <- molIon$cameraobj@xcmsSet@phenoData + getPvalue <- function(dataidx) { + aov.data <- data.frame(resp=as.numeric(peaklist[dataidx,coords]), class=class) + anova(aov(resp~class, aov.data))$Pr[1] + } + testname <- "anova p-value" + ans[ans[,6]!="",5] <- sapply(figidx, getPvalue) + } + + header <- matrix(c("Proposed Mass","Most probable Compound","Probability","Entropy", testname,"EIC-plot", "Ion annotation",coords), nrow=1 , ncol=7+length(coords) ) + ans <- rbind(header, ans) + + + # additional field + # ans <- cbind(ans[,1:2], ans[,2], ans[,3:ncol(ans)]) + #ans[ans[,3]!="unknown",][-1,3] <- as.character(DB$sbml.id[nid]) + + if(html) { + #require(hwriter) + ansb <- ans + ans[ans[,2]!="unknown",][-1,2] <- as.character(DB$name[nid]) + if(linkPattern=="pubchem") ansb <- ans + + hyper=matrix(paste(linkURL, ansb[-1,2], sep=""),ncol=1 ) + if(!is.null(molIon$cameraobj)) { + hyper1=matrix(paste(fig, ans[-1,6],".png", sep=""),ncol=1 ) + } + else { + hyper1 <- ans[-1,6] + hyper1[ans[-1,6]!=""][allidx[,2]!="neg"] <- paste(hyper1[ans[-1,6]!=""][allidx[,2]!="neg"], "pos", sep="") + hyper1[ans[-1,6]!=""][allidx[,2]=="neg"] <- paste(hyper1[ans[-1,6]!=""][allidx[,2]=="neg"], "neg", sep="") + hyper1=matrix(paste(fig, hyper1,".png", sep=""),ncol=1 ) + } + p=openPage(paste(filename,".html",sep="")) + ans2 <- ans[,1:7] + link <- cbind(matrix(NA,nrow(ans2),1),rbind(NA,hyper),matrix(NA,nrow(ans2),3),rbind(NA,hyper1),matrix(NA,nrow(ans2),1)) + # This block is responsible to add as many columns as the user + # wants + if(!is.null(addLink)){ + for(l in 1:length(addLink$link)) { + link <- cbind(link, rbind(NA, addLink[[l]])) + } + for(a in 1:length(addLink$ans)) { + ans2 <- cbind(ans2,addLink$ans[[a]]) + #colnames(ans2)[7+a] <- addLink$ans[[a]][1] + } + } + hwrite(ans2, p,row.bgcolor='#ffdc98', link=link ) + closePage(p) + if(!is.null(molIon$cameraobj)) { + plotEIC(molIon$cameraobj@xcmsSet, figidx, ans[ans[,6]!="",6][-1], colorplot=colorplot) + } + else { + dataidxP <- as.numeric(allidx[allidx[,2]!="neg",1]) + pngidxP <- allidx[allidx[,2]!="neg",3] + plotEIC(molIon$pos@xcmsSet, dataidxP, pngidxP, "pos", colorplot=colorplot) + dataidxN <- as.numeric(allidx[allidx[,2]=="neg",1]) + pngidxN <- allidx[allidx[,2]=="neg",3] + plotEIC(molIon$neg@xcmsSet, dataidxN, pngidxN, "neg", colorplot=colorplot) + } + + } + else { + ansb <- ans + } + colnames(ansb) <- ansb[1,] + ansb <- ansb[-1,] + return(list(classTable=ansb, figidx=figidx)) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,323 @@ +# lib.r ProbMetab version="1.0.0" +# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr +# Contributors: Yann Guitton and Jean-francois Martin + + +##Main probmetab function launch by the Galaxy ProbMetab wrapper +probmetab = function(xa, xaP, xaN, variableMetadata, variableMetadataP, variableMetadataN, listArguments){ + ##ONE MODE ACQUISITION## + if(listArguments[["mode_acquisition"]]=="one") { + comb=NULL + + #Get the polarity from xa object + polarity=xa@polarity + #SNR option + if ("xsetnofill" %in% names(listArguments)) { + load(listArguments[["xsetnofill"]]) + xsetnofill=xset + } + else{ + xsetnofill=NULL + } + #Exclude samples + if ("toexclude" %in% names(listArguments)) { + toexclude=listArguments[["toexclude"]] + } + else { + toexclude=NULL + } + ionAnnot=get.annot(xa, polarity=polarity, allowMiss=listArguments[["allowMiss"]],xset=xsetnofill,toexclude=toexclude) + comb=NULL + } + + ##TWO MODES ACQUISITION## + #Mode annotatediffreport + else if(listArguments[["inputs_mode"]]=="two"){ + ##Prepare the objects that will be used for the get.annot function + comb=1 + + + xsetPnofill=NULL + xsetNnofill=NULL + # TODO: a reactiver + #if ("xsetPnofill" %in% names(listArguments)) { + # load(listArguments[["xsetPnofill"]]) + # xsetPnofill=xset + #} + #if ("xsetNnofill" %in% names(listArguments)) { + # load(listArguments[["xsetNnofill"]]) + # xsetNnofill=xset + #} + # include CAMERA non-annotated compounds, and snr retrieval + # comb 2+ - used on Table 1 + ionAnnotP2plus = get.annot(axP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]]) + ionAnnotN2plus = get.annot(axN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]]) + ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus) + print(sum(ionAnnot$molIon[,3]==1)) + print(sum(ionAnnot$molIon[,3]==0)) + write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv") + #Merge variableMetadata Negative and positive acquisitions mode + + + #Mode combinexsannos TODO bug avec tableau issus de combinexsannos + #else { + #load(listArguments[["image_combinexsannos"]]) + #image_combinexsannos=cAnnot + ##Prepare the objects that will be used for the combineMolIon function + #load(listArguments[["image_pos"]]) + #image_pos=xa + #ionAnnot=combineMolIon(peaklist=cAnnot, cameraobj=image_pos, polarity="pos") + #} + + } + + ##DATABASE MATCHING## + if (listArguments[["kegg_db"]]=="KEGG"){ + DB=build.database.kegg(orgID = NULL) + } + else{ + table_list <<- NULL + ids=strsplit(listArguments[["kegg_db"]],",") + ids=ids[[1]] + if(length(ids)>1){ + for(i in 1:length(ids)){ + table_list[[i]] <- build.database.kegg(ids[i]) + } + db_table=do.call("rbind",table_list) + DB=unique(db_table) + } + else{ + DB=build.database.kegg(listArguments[["kegg_db"]]) + } + } + #Matching des mass exactes mesurees avec les masses des compounds KEGG (pas M+H ou M-H) + reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]]) + ##PROBABILITY RANKING## + # number of masses with candidates inside the fixed mass window + # and masses with more than one candidate + length(unique(reactionM[reactionM[,"id"]!="unknown",1])) + sum(table(reactionM[reactionM[,"id"]!="unknown",1])>1) + #if (listArguments[["useIso"]]){ + #BUG TODO + # Calculate the ratio between observed and theoretical isotopic patterns. + # If you don't have an assessment of carbon offset to carbon number prediction + # skip this step and use the reactionM as input to weigthM function. + #isoPatt < incorporate.isotopes(comb2plus, reactionM, , samp=12:23, DB=DB) + # calculate the likelihood of each mass to compound assignment using mass accuracy,and isotopic pattern, when present + #wl < weightM(isoPatt,intervals=seq(0,1000,by=500), offset=c(3.115712, 3.434146, 2.350798)) + + #isoPatt=incorporate.isotopes(ionAnnot, reactionM,comb=comb,var=listArguments[["var"]],DB=DB) + + #wl = weightM(reactionM, useIso=true) + #} + #else { + #wl = weightM(reactionM, useIso=FALSE) + #} + wl =weightM(reactionM, useIso=FALSE) + w = design.connection(reactionM) + # Probability calculations + x = 1:ncol(wl$wm) + y = 1:nrow(wl$wm) + conn = gibbs.samp(x, y, 5000, w, wl$wm) + ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]]) + if(listArguments[["html"]]){ + #Zip the EICS plot + system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"')) + } + + # calculate the correlations and partial correlations and cross reference then with reactions + mw=which(w==1,arr.ind=TRUE) + #reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial + #correlation in a user defined threshold of false discovery rate for significance testing. After the + #correlation test the function also overlay significant correlations with all putative reactions between + #two masses. + #It generates a list of estimated correlations and reactions. + corList=reac2cor(mw,ansConn$classTable,listArguments[["opt"]],listArguments[["corths"]],listArguments[["corprob"]],listArguments[["pcorprob"]]) + ans=list("ansConn"=ansConn,"corList"=corList) + #Generate the siff table for CytoScape + cytoscape_output(corList,ansConn) + + + #Execute the merge_probmetab function to merge the variableMetadata table and annotations from ProbMetab results + + if(listArguments[["mode_acquisition"]]=="one") { + #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt) + names(variableMetadata)[names(variableMetadata)=="mzmed"] <- "mz" + names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt" + variableM=merge_probmetab(variableMetadata, ansConn) + write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv") + } else if (listArguments[["mode_acquisition"]]=="two") { + #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt) + names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz" + names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt" + names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz" + names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt" + variableMP=merge_probmetab(variableMetadataP, ansConn) + write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv") + variableMN=merge_probmetab(variableMetadataN, ansConn) + write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv") + } + + return(ans) + +} + +##Function that generates a siff table for CytoScape +cytoscape_output=function(corList,ansConn){ + signif_cor=as.data.frame(corList$signif.cor) + classTable=as.data.frame(ansConn$classTable) + #Siff table + siff_table=cbind(signif_cor["node1"],signif_cor["cor"],signif_cor["node2"]) + #attribute table output for Cytoscape + + ## START Code part from the export2cytoscape function of ProbMetab written by Ricardo R. Silva + for (i in 1:nrow(classTable)) if (classTable[i, 1] == ""){ + classTable[i, c(1, 4, 6, 7)] <- classTable[i - 1, c(1, 4, 6, 7)] + } + msel <- as.matrix(classTable[, 1:7]) + msel <- cbind(msel[, 6], msel[,-6]) + colnames(msel)[1] <- "Id" + msel[, 1] <- sub("^\\s+", "", msel[, 1]) + colnames(msel)[1] <- "Id" + ids <- unique(msel[, 1]) + attrMatrix <- matrix("", nrow = length(ids), ncol = ncol(msel)-1) + for (i in 1:length(ids)) { + attrMatrix[i, 1] <- unique(msel[msel[, 1] == ids[i], + 2]) + attrMatrix[i, 2] <- paste("[", paste(msel[msel[, + 1] == ids[i], 3], collapse = ", "), "]", sep = "") + attrMatrix[i, 3] <- paste("[", paste(msel[msel[, + 1] == ids[i], 4], collapse = ", "), "]", sep = "") + attrMatrix[i, 4] <- unique(msel[msel[, 1] == ids[i], + 5]) + attrMatrix[i, 5] <- paste("[", paste(msel[msel[, + 1] == ids[i], 6], collapse = ", "), "]", sep = "") + attrMatrix[i, 6] <- unique(msel[msel[, 1] == ids[i], + 7]) + } + ids <- as.numeric(unique(msel[, 1])) + attrMatrix <- cbind(ids, attrMatrix) + colnames(attrMatrix) <- colnames(msel) + ## END Code part from the export2cytoscape function of ProbMetab writieen by Ricardo R. Silva + write.table(attrMatrix, sep="\t", quote=FALSE, row.names=FALSE, file="Analysis_Report.tsv") + write.table(siff_table, sep="\t", quote=FALSE, row.names=FALSE, file="sif.tsv") + + return(attrMatrix) +} + +##Functions written by Jean-Francois Martin + +deter_ioni <- function (aninfo, pm) +{ + # determine ionisation in ProbMetab result file, used in function merge_probmetab + # input : for 1 ion, aninfo = string with m/z rt and CAMERA annotation from ProbMetab result file + # if the difference between m/z and the probmetab proposed mass is ~1 we use the sign (positive or negative) of this diference + # to define the type of ionisation + # If adduct or fragment was detected, therefore diff >>1 and so, we search for substring "+" ou "2+" ou "3+" ou "-"... + # to define the type of ionisation + # aninfo : vecteur of character resulting of the parsing(sep="#") of the probmetab annotation + if (round(abs(as.numeric(aninfo[1]) - pm),0) ==1) { + if (as.numeric(aninfo[1]) - pm <0) {esi <- "n"} else {esi <- "p"} + } else + if (!is.na(aninfo[4])) { + anstr <- aninfo[4] + # cat(anstr) + if ((grepl("]+",anstr,fixed=T)==T) || (grepl("]2+",anstr,fixed=T)==T) || (grepl("]3+",anstr,fixed=T)==T)) { esi <- "p"} + else + if ((grepl("]-",anstr,fixed=T)==T) || (grepl("]2-",anstr,fixed=T)==T) || (grepl("]3-",anstr,fixed=T)==T)) { esi <- "n"} + # cat(" ioni ",esi,"\n") + } else + { esi <- "u"} + + return(esi) +} + + +merge_probmetab <- function(metaVar,ansConn) { + ## Parse ProbMetab information result file and merge in variable_metaData initial file + ## inputs : + ## metaVar : data.frame of metadataVariable input of probmetab function + ## ansConn : data.frame of ProbMetab result + ## output : dataframe with Probmetab results merge with variableMetadata + ## Constante + ## iannot : indice de la colonne annotation dans le resultat de probMetab + iannot <- 4 + + ## definition of an unique identification of ions mz with 3 decimals and rt(sec) with 1 decimal to avoid + ## duplicate ions name in the diffreport result file + ions <- paste ("M",round(metaVar$mz,3),"T",round(metaVar$rt,1),sep="") + metaVar <- data.frame(ions,metaVar) + + ###### Result data.frame from ProbMetab result list + an_ini <- ansConn$classTable + + ## Suppression of rows without mz and rt or unknown and columns of intensities + ## COLUMNS SUBSCRIPTS HAVE TO BE CHECKED WITh DIFFERENT RESULTS FILES + an <- an_ini[(an_ini[,2]!="unknown"),c(1,2,3,7)] + ## initialisation of vectors receiving the result of the parse of the column annotation (subscrip iannot) + mz <- rep(0,dim(an)[1]) + rt <- rep(0,dim(an)[1]) + propmz <- rep(0,dim(an)[1]) + ioni <- rep("u",dim(an)[1]) + + ## parse the column annotation and define ionisation mode + for (i in 1:dim(an)[1]) { + if (an[i,1] != "") { + info_mzrt <- unlist(strsplit(an[i,iannot],"#")) + propmz[i] <- as.numeric(an[i,1]) + mz[i] <- as.numeric(info_mzrt[1]) + rt[i] <- as.numeric(info_mzrt[2]) + ioni[i] <- deter_ioni(info_mzrt,as.numeric(an[i,1])) + } + else { + propmz[i] <- as.numeric(propmz[i-1]) + mz[i] <- as.numeric(mz[i-1]) + rt[i] <- as.numeric(rt[i-1]) + ioni[i] <- ioni[i-1] + } + } + + ## definition of an unique identification of ions : mz with 3 decimals and rt(sec) with 1 decimal + ## The same as for the metadataVariable data.frame to match with. + ions <- paste ("M",round(mz,3),"T",round(rt,1),sep="") + an <- data.frame(ions,ioni,propmz,mz,rt,an) + + ## transposition of the different probmetab annotations which are in different rows in the initial result data.frame + ## on only 1 row separated with a ";" + li <- as.matrix(table(an$propmz)) + li <- data.frame(dimnames(li)[1],li) + dimnames(li)[[2]][1] <- "propmz" + ions <- rep("u",dim(li)[1]) + propmz <- rep(0,dim(li)[1]) + mpc <- rep("c",dim(li)[1]) + proba <- rep("p",dim(li)[1]) + c <- 0 + while (c < dim(li)[1]) { + c <- c + 1 + suban <- an[an$propmz==li[c,1],] + ions[c] <- as.character(suban[1,1]) + propmz[c] <- as.numeric(suban[1,3]) + mpc[c] <- paste(suban[,7],collapse=";") + proba[c] <- paste(as.character(suban[,8]),collapse=";") + } + + ## Creation of the data.frame with 1 row per ions + anc <- data.frame(ions,propmz,mpc,proba) + anc <- anc[order(anc[,1]),] + + metaVarFinal <- merge(metaVar, anc, by.x=1, by.y=1, all.x=T, all.y=T) + metaVarFinal <- metaVarFinal[,-1] + #write.table(metaVarFinal,file="res.txt", sep="\t", row.names=F, quote=F) + + return (metaVarFinal) +} + +# RETROCOMPATIBILITE avec ancienne version de annotate +getVariableMetadata = function(xa) { + # --- variableMetadata --- + peakList=getPeaklist(xa) + peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); + variableMetadata=peakList[,!(colnames(peakList) %in% c(sampnames(xa@xcmsSet)))] + variableMetadata$name= paste("M",round(variableMetadata$mz),"T",round(variableMetadata$rt),sep="") + return (variableMetadata) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nohup.out Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,1683 @@ +git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 +cd /tmp/tmpw4QiHm; git clone --branch 'master' '/home/fr2424/sib/lecorguille/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +Initialized empty Git repository in /tmp/tmpw4QiHm/galaxy-dev/.git/ +Set COMMON_STARTUP_ARGS to --dev-wheels +Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample +Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample +Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample +Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample +Initializing lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml from user_info.xml.sample +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample +Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample +Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample +Initializing tool-data/add_scores.loc from add_scores.loc.sample +Initializing tool-data/alignseq.loc from alignseq.loc.sample +Initializing tool-data/all_fasta.loc from all_fasta.loc.sample +Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample +Initializing tool-data/binned_scores.loc from binned_scores.loc.sample +Initializing tool-data/codingSnps.loc from codingSnps.loc.sample +Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample +Initializing tool-data/faseq.loc from faseq.loc.sample +Initializing tool-data/funDo.loc from funDo.loc.sample +Initializing tool-data/liftOver.loc from liftOver.loc.sample +Initializing tool-data/maf_index.loc from maf_index.loc.sample +Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample +Initializing tool-data/microbial_data.loc from microbial_data.loc.sample +Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample +Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample +Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample +Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample +Initializing tool-data/phastOdds.loc from phastOdds.loc.sample +Initializing tool-data/picard_index.loc from picard_index.loc.sample +Initializing tool-data/quality_scores.loc from quality_scores.loc.sample +Initializing tool-data/regions.loc from regions.loc.sample +Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample +Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample +Initializing tool-data/sift_db.loc from sift_db.loc.sample +Initializing tool-data/srma_index.loc from srma_index.loc.sample +Initializing tool-data/twobit.loc from twobit.loc.sample +Initializing static/welcome.html from welcome.html.sample +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +Ignoring indexes: https://pypi.python.org/simple +/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. + SNIMissingWarning +/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. + InsecurePlatformWarning +Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) +Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) +Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) +Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) +Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) +Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) +Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) +Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) +You are using pip version 8.0.2+gx2, however version 8.1.2 is available. +You should consider upgrading via the 'pip install --upgrade pip' command. +Requirement already satisfied (use --upgrade to upgrade): nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) +Requirement already satisfied (use --upgrade to upgrade): NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): funcsigs>=1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +You are using pip version 8.0.2+gx2, however version 8.1.2 is available. +You should consider upgrading via the 'pip install --upgrade pip' command. +Testing using galaxy_root /tmp/tmpw4QiHm/galaxy-dev +Testing tools with command [cd /tmp/tmpw4QiHm/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /projet/fr2424/sib/lecorguille/script/git/w4m/probmetab/galaxy/probmetab/tool_test_output.html --xunit_report_file /tmp/tmpw4QiHm/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/probmetab/galaxy/probmetab/tool_test_output.json functional.test_toolbox] +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +Ignoring indexes: https://pypi.python.org/simple +/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. + SNIMissingWarning +/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. + InsecurePlatformWarning +Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) +Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) +Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) +Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) +Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) +Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) +Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) +Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) +You are using pip version 8.0.2+gx2, however version 8.1.2 is available. +You should consider upgrading via the 'pip install --upgrade pip' command. +Requirement already satisfied (use --upgrade to upgrade): nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) +Requirement already satisfied (use --upgrade to upgrade): NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): funcsigs>=1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +You are using pip version 8.0.2+gx2, however version 8.1.2 is available. +You should consider upgrading via the 'pip install --upgrade pip' command. +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +DEBUG:galaxy.app:python path is: /tmp/tmpw4QiHm/galaxy-dev/lib, /tmp/tmpw4QiHm/galaxy-dev/lib, /tmp/tmpw4QiHm/galaxy-dev/test, /tmp/tmpw4QiHm/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages +INFO:galaxy.config:Logging at '10' level to 'stdout' +[('app:main', 'new_file_path', '/tmp/tmp_QwDNn/tmpbNtbsc/new_files_path_Tda93T'), ('app:main', 'database_connection', 'sqlite:////tmp/tmp_QwDNn/tmpbNtbsc/database/universe.sqlite'), ('app:main', 'data_manager_config_file', 'config/data_manager_conf.xml.sample,test/functional/tools/sample_data_manager_conf.xml'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'allow_user_deletion', True), ('app:main', 'master_api_key', 'test_key'), ('app:main', 'tool_config_file', 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+migrate.versioning.script.base DEBUG 2016-05-17 23:18:39,164 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... +migrate.versioning.script.base DEBUG 2016-05-17 23:18:39,164 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully +migrate.versioning.repository DEBUG 2016-05-17 23:18:39,164 Repository lib/galaxy/model/migrate loaded successfully +migrate.versioning.repository DEBUG 2016-05-17 23:18:39,164 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) +galaxy.model.migrate.check INFO 2016-05-17 23:18:39,190 Migrating 127 -> 128... +galaxy.model.migrate.check INFO 2016-05-17 23:18:39,744 +galaxy.model.migrate.check INFO 2016-05-17 23:18:39,745 Migration script to add session update time (used for timeouts) +galaxy.model.migrate.check INFO 2016-05-17 23:18:39,745 +galaxy.model.migrate.check INFO 2016-05-17 23:18:39,745 +galaxy.model.migrate.check INFO 2016-05-17 23:18:39,746 Migrating 128 -> 129... +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,290 +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,291 Migration script to allow invalidation of job external output metadata temp files +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,291 +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,291 +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,291 Migrating 129 -> 130... +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,914 +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,914 Migration script to change the value column of user_preference from varchar to text. +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,914 +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,914 +galaxy.model.migrate.check INFO 2016-05-17 23:18:40,915 Migrating 130 -> 131... +galaxy.model.migrate.check INFO 2016-05-17 23:18:41,812 +galaxy.model.migrate.check INFO 2016-05-17 23:18:41,812 Migration script to support subworkflows and workflow request input parameters +galaxy.model.migrate.check INFO 2016-05-17 23:18:41,812 +galaxy.model.migrate.check INFO 2016-05-17 23:18:41,812 +galaxy.config INFO 2016-05-17 23:18:41,829 Install database targetting Galaxy's database configuration. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,894 Loading datatypes from ./config/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,894 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,896 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,899 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,899 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,899 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,900 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,901 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,902 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,902 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,902 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,902 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,902 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,903 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,904 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,905 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,905 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,905 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,905 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,906 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,906 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,906 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,906 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,906 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,906 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,907 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,910 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,910 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,910 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,910 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,911 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,912 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,913 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,914 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,915 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,916 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,917 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,923 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,924 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,926 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,926 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,927 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,928 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,929 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,930 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,931 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,932 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,933 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,934 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,937 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,938 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,939 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,939 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,939 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,939 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,939 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,939 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,941 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,942 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,942 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,942 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,942 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,945 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,946 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,947 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,948 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,949 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,950 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,951 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,952 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,952 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,952 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,952 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,952 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:41,952 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt +galaxy.jobs WARNING 2016-05-17 23:18:42,000 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/tmp_QwDNn/functional_tests_wsgi.ini" instead +galaxy.jobs DEBUG 2016-05-17 23:18:42,000 Loading job configuration from /tmp/tmp_QwDNn/functional_tests_wsgi.ini +galaxy.jobs DEBUG 2016-05-17 23:18:42,000 Done loading job configuration +beaker.container DEBUG 2016-05-17 23:18:42,137 data file /tmp/tmpw4QiHm/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache +galaxy.tools.toolbox.watcher INFO 2016-05-17 23:18:42,138 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-05-17 23:18:42,138 Parsing the tool configuration /tmp/tmpw4QiHm/tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-05-17 23:18:42,145 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-05-17 23:18:42,162 Loaded tool id: Probmetab, version: 1.0.1 into tool panel.. +galaxy.tools.toolbox.base INFO 2016-05-17 23:18:42,185 Parsing the tool configuration /tmp/tmpw4QiHm/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-05-17 23:18:42,186 Parsing the tool configuration /tmp/tmpw4QiHm/empty_tool_conf.xml +galaxy.tools.deps WARNING 2016-05-17 23:18:42,186 Path '/tmp/tmpw4QiHm/deps' does not exist, ignoring +galaxy.tools.deps WARNING 2016-05-17 23:18:42,186 Path '/tmp/tmpw4QiHm/deps' is not directory, ignoring +galaxy.tools.search DEBUG 2016-05-17 23:18:42,255 Starting to build toolbox index. +galaxy.tools.search DEBUG 2016-05-17 23:18:42,462 Toolbox index finished. +galaxy.tools.data_manager.manager DEBUG 2016-05-17 23:18:42,465 Loaded Data Manager: test_data_manager +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,467 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,468 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-05-17 23:18:42,470 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,470 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,470 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,471 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,471 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,473 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,473 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,475 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,475 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,479 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-05-17 23:18:42,480 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,480 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,481 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,485 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,490 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,492 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-05-17 23:18:42,493 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,493 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,495 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,497 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-05-17 23:18:42,498 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,498 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,499 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,499 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-05-17 23:18:42,501 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,501 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,501 Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,501 Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,502 Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,503 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,504 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,505 Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,506 Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,507 Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,507 Loaded converter: CONVERTER_bed_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,508 Loaded converter: CONVERTER_bed_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,509 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,510 Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,510 Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,511 Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,512 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,513 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,513 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,514 Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,515 Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,516 Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,517 Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,517 Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,518 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,519 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,519 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,520 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,521 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,521 Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,522 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,523 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,524 Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,524 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,525 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,526 Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,527 Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,527 Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,528 Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,529 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,530 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,530 Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,531 Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,532 Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,532 Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,533 Loaded converter: CONVERTER_encodepeak_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,534 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,535 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,535 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,536 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,537 Loaded converter: CONVERTER_sam_to_bam +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,538 Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,539 Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,539 Loaded converter: CONVERTER_vcf_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,540 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,541 Loaded converter: CONVERTER_vcf_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,542 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,542 Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,543 Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,544 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,544 Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,545 Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,546 Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,547 Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2016-05-17 23:18:42,548 Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2016-05-17 23:18:42,554 Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2016-05-17 23:18:42,555 Loaded history export tool: __EXPORT_HISTORY__ +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,556 VisualizationsRegistry, loaded plugin: charts +galaxy.visualization.plugins.config_parser INFO 2016-05-17 23:18:42,556 Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2016-05-17 23:18:42,557 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,557 VisualizationsRegistry, loaded plugin: csg +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,557 VisualizationsRegistry, loaded plugin: graphview +galaxy.visualization.plugins.config_parser INFO 2016-05-17 23:18:42,558 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,558 VisualizationsRegistry, loaded plugin: graphviz +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,559 VisualizationsRegistry, loaded plugin: phyloviz +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,559 VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2016-05-17 23:18:42,559 Visualizations plugin disabled: Sweepster. Skipping... +galaxy.web.base.pluginframework INFO 2016-05-17 23:18:42,560 VisualizationsRegistry, loaded plugin: trackster +galaxy.tours INFO 2016-05-17 23:18:42,590 Loaded tour 'core.galaxy_ui' +galaxy.tours INFO 2016-05-17 23:18:42,612 Loaded tour 'core.history' +galaxy.jobs.manager DEBUG 2016-05-17 23:18:42,622 Starting job handler +galaxy.jobs INFO 2016-05-17 23:18:42,622 Handler 'main' will load all configured runner plugins +galaxy.jobs.runners.state_handler_factory DEBUG 2016-05-17 23:18:42,624 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-05-17 23:18:42,624 Starting 5 LocalRunner workers +galaxy.jobs DEBUG 2016-05-17 23:18:42,625 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.runners.state_handler_factory DEBUG 2016-05-17 23:18:42,627 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-05-17 23:18:42,627 Starting 2 TaskRunner workers +galaxy.jobs DEBUG 2016-05-17 23:18:42,627 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' +galaxy.jobs DEBUG 2016-05-17 23:18:42,627 Legacy destination with id 'local:///', url 'local:///' converted, got params: +galaxy.jobs.handler DEBUG 2016-05-17 23:18:42,628 Loaded job runners plugins: tasks:local +galaxy.jobs.handler INFO 2016-05-17 23:18:42,628 job handler stop queue started +galaxy.jobs.handler INFO 2016-05-17 23:18:42,641 job handler queue started +galaxy.sample_tracking.external_service_types DEBUG 2016-05-17 23:18:42,646 Loaded external_service_type: Simple unknown sequencer 1.0.0 +galaxy.sample_tracking.external_service_types DEBUG 2016-05-17 23:18:42,647 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 +galaxy.workflow.scheduling_manager DEBUG 2016-05-17 23:18:42,662 Starting workflow schedulers +functional_tests.py INFO 2016-05-17 23:18:42,668 Embedded Universe application started +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,716 Enabling 'library' controller, class: Library +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,716 Enabling 'error' controller, class: Error +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,720 Enabling 'biostar' controller, class: BiostarController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,733 Enabling 'workflow' controller, class: WorkflowController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,734 Enabling 'tag' controller, class: TagsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,749 Enabling 'requests_admin' controller, class: RequestsAdmin +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,749 Enabling 'library_common' controller, class: LibraryCommon +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,751 Enabling 'data_manager' controller, class: DataManager +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,761 Enabling 'user' controller, class: User +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,761 Enabling 'requests_common' controller, class: RequestsCommon +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,770 Enabling 'history' controller, class: HistoryController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,772 Enabling 'library_admin' controller, class: LibraryAdmin +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,779 Enabling 'dataset' controller, class: DatasetInterface +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,783 Enabling 'forms' controller, class: Forms +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,784 Enabling 'tool_runner' controller, class: ToolRunner +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,784 Enabling 'external_services' controller, class: ExternalServiceController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,785 Enabling 'mobile' controller, class: Mobile +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,786 Enabling 'userskeys' controller, class: User +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,788 Enabling 'external_service' controller, class: ExternalService +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,805 Enabling 'admin' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,925 Enabling 'admin_toolshed' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,925 Enabling 'admin_toolshed' controller, class: AdminToolshed +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,926 Enabling 'requests' controller, class: Requests +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,927 Enabling 'search' controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,930 Enabling 'request_type' controller, class: RequestType +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,935 Enabling 'page' controller, class: PageController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,941 Enabling 'visualization' controller, class: VisualizationController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,945 Enabling 'root' controller, class: RootController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,946 Enabling 'async' controller, class: ASync +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,951 Enabling 'libraries' API controller, class: LibrariesController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,952 Enabling 'quotas' API controller, class: QuotaAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,955 Enabling 'history_contents' API controller, class: HistoryContentsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,959 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,960 Enabling 'authenticate' API controller, class: AuthenticationController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,961 Enabling 'tool_data' API controller, class: ToolData +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,961 Enabling 'job_files' API controller, class: JobFilesAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,962 Enabling 'group_users' API controller, class: GroupUsersAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,964 Enabling 'folders' API controller, class: FoldersController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,965 Enabling 'groups' API controller, class: GroupAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,967 Enabling 'datasets' API controller, class: DatasetsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,969 Enabling 'jobs' API controller, class: JobController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,970 Enabling 'visualizations' API controller, class: VisualizationsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,972 Enabling 'folder_contents' API controller, class: FolderContentsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,973 Enabling 'forms' API controller, class: FormDefinitionAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,976 Enabling 'tools' API controller, class: ToolsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,976 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,977 Enabling 'tours' API controller, class: ToursController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,979 Enabling 'histories' API controller, class: HistoriesController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,980 Enabling 'pages' API controller, class: PagesController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,981 Enabling 'roles' API controller, class: RoleAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,981 Enabling 'genomes' API controller, class: GenomesController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,984 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:42,985 Enabling 'requests' API controller, class: RequestsAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,007 Enabling 'search' API controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,008 Enabling 'users' API controller, class: UserAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,009 Enabling 'group_roles' API controller, class: GroupRolesAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,010 Enabling 'metrics' API controller, class: MetricsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,011 Enabling 'datatypes' API controller, class: DatatypesController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,012 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,014 Enabling 'remote_files' API controller, class: RemoteFilesAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,015 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,015 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,016 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,016 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,016 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,017 Enabling 'samples' API controller, class: SamplesAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,018 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,018 Enabling 'history_tags' API controller, class: HistoryTagsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,018 Enabling 'workflow_tags' API controller, class: WorkflowTagsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,021 Enabling 'library_contents' API controller, class: LibraryContentsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,021 Enabling 'page_revisions' API controller, class: PageRevisionsController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,024 Enabling 'workflows' API controller, class: WorkflowsAPIController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,025 Enabling 'configuration' API controller, class: ConfigurationController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,026 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,026 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController +galaxy.web.framework.base DEBUG 2016-05-17 23:18:43,027 Enabling 'request_types' API controller, class: RequestTypeAPIController +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,266 Enabling 'httpexceptions' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,267 Enabling 'recursive' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,279 Enabling 'error' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,279 Enabling 'x-forwarded-host' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,279 Enabling 'Request ID' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,285 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,285 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,286 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,286 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-05-17 23:18:43,286 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static +galaxy.queue_worker INFO 2016-05-17 23:18:43,286 Binding and starting galaxy control worker for main +functional_tests.py DEBUG 2016-05-17 23:18:43,292 Attempting to serve app on randomly chosen port: 8809 +/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + 'storage.' % (dialect.name, dialect.driver)) +functional_tests.py INFO 2016-05-17 23:18:43,521 Embedded web server started +functional_tests.py INFO 2016-05-17 23:18:43,521 Functional tests will be run against localhost:8809 +[?1034hbase.asserts DEBUG 2016-05-17 23:18:43,604 base.asserts.text +base.asserts DEBUG 2016-05-17 23:18:43,605 base.asserts.tabular +base.asserts DEBUG 2016-05-17 23:18:43,605 base.asserts.xml +nose.plugins.manager DEBUG 2016-05-17 23:18:43,611 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML +ProbMetab Tool ( Probmetab ) > Test-1 ... requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:43,655 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-05-17 23:18:43,658 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:43,667 "GET /api/users?key=test_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:43,691 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-05-17 23:18:43,693 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,052 "POST /api/users HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,053 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-05-17 23:18:44,056 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,100 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,101 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,218 "POST /api/histories HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,223 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-05-17 23:18:44,278 Validated and populated state for tool request (12.441 ms) +galaxy.tools.actions.upload DEBUG 2016-05-17 23:18:44,312 Persisted uploads (16.736 ms) +galaxy.tools.actions.upload DEBUG 2016-05-17 23:18:44,567 Checked and cleaned uploads (255.374 ms) +galaxy.tools.actions.upload_common INFO 2016-05-17 23:18:44,630 tool upload1 created job id 1 +galaxy.tools.actions.upload DEBUG 2016-05-17 23:18:44,710 Created upload job (142.419 ms) +galaxy.tools.execute DEBUG 2016-05-17 23:18:44,710 Tool [upload1] created job [1] (414.938 ms) +galaxy.tools.execute DEBUG 2016-05-17 23:18:44,724 Executed all jobs for tool request: (446.076 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,751 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,752 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,811 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,813 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,876 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,877 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-05-17 23:18:44,912 (1) Working directory for job is: /tmp/tmpw4QiHm/job_working_directory/000/1 +galaxy.jobs.handler DEBUG 2016-05-17 23:18:44,934 (1) Dispatching to local runner +galaxy.jobs DEBUG 2016-05-17 23:18:44,981 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:44,996 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:44,997 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-05-17 23:18:45,038 Job [1] queued (103.400 ms) +galaxy.jobs.handler INFO 2016-05-17 23:18:45,063 (1) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:45,168 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:45,169 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:45,339 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:45,341 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,462 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,462 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,462 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,463 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps WARNING 2016-05-17 23:18:45,463 Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:45,466 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:45,468 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-05-17 23:18:45,532 Built script [/tmp/tmpw4QiHm/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/tmpw4QiHm/galaxy-dev/tools/data_source/upload.py /tmp/tmpw4QiHm/galaxy-dev /tmp/tmpw4QiHm/tmp/tmpguw7h9 /tmp/tmpw4QiHm/tmp/tmprRgOLi 1:/tmp/tmpw4QiHm/job_working_directory/000/1/dataset_1_files:/tmp/tmpw4QiHm/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:45,599 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:45,603 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:45,766 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:45,768 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,855 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,855 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,855 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps DEBUG 2016-05-17 23:18:45,855 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps WARNING 2016-05-17 23:18:45,855 Failed to resolve dependency on 'samtools', ignoring +galaxy.jobs.runners DEBUG 2016-05-17 23:18:45,882 (1) command is: /tmp/tmpw4QiHm/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/tmpw4QiHm/job_working_directory/000/1/set_metadata_uAINzL.py" "/tmp/tmpw4QiHm/tmp/tmpguw7h9" "/tmp/tmpw4QiHm/job_working_directory/000/1/galaxy.json" "/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1__6F4ZW,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_IAQkOq,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_wdkcNz,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_Fx0LLf,/tmp/tmpw4QiHm/files/000/dataset_1.dat,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_FiInlP" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-05-17 23:18:45,898 (1) executing job script: /tmp/tmpw4QiHm/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:45,898 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:45,909 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-05-17 23:18:45,914 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,074 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,081 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,196 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,198 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,258 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,260 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,320 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,321 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,385 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,387 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,454 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,456 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,523 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,525 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,588 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,589 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,651 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,653 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,716 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,717 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,803 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,805 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,867 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,868 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:46,948 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:46,949 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,011 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,013 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,075 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,076 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,179 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,180 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,239 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,240 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,305 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,306 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,372 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,373 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,435 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,437 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,505 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,507 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,572 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,573 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,635 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,637 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,700 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,701 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,764 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,765 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,827 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,828 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,890 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,891 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:47,969 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:47,970 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,033 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,034 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,098 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,099 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,164 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,165 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,245 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,246 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,308 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,310 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-05-17 23:18:48,348 execution finished: /tmp/tmpw4QiHm/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,438 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,440 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-05-17 23:18:48,584 loading metadata from file for: HistoryDatasetAssociation 1 +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,613 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,614 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:48,763 "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:48,765 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-05-17 23:18:48,910 Validated and populated state for tool request (73.065 ms) +galaxy.jobs DEBUG 2016-05-17 23:18:48,963 job 1 ended (finish() executed in (614.591 ms)) +galaxy.tools.actions INFO 2016-05-17 23:18:49,016 Handled output (76.304 ms) +galaxy.tools.actions INFO 2016-05-17 23:18:49,060 Handled output (43.535 ms) +galaxy.tools.actions INFO 2016-05-17 23:18:49,104 Handled output (44.088 ms) +galaxy.tools.actions INFO 2016-05-17 23:18:49,156 Handled output (51.731 ms) +galaxy.tools.actions INFO 2016-05-17 23:18:49,207 Handled output (51.534 ms) +galaxy.tools.actions INFO 2016-05-17 23:18:49,349 Handled output (138.001 ms) +galaxy.tools.actions INFO 2016-05-17 23:18:49,413 Verified access to datasets (5.855 ms) +galaxy.tools.execute DEBUG 2016-05-17 23:18:49,470 Tool [Probmetab] created job [2] (536.500 ms) +galaxy.tools.execute DEBUG 2016-05-17 23:18:49,483 Executed all jobs for tool request: (572.932 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:49,597 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:49,598 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:49,710 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:49,912 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:50,022 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.jobs DEBUG 2016-05-17 23:18:50,265 (2) Working directory for job is: /tmp/tmpw4QiHm/job_working_directory/000/2 +galaxy.jobs.handler DEBUG 2016-05-17 23:18:50,276 (2) Dispatching to local runner +galaxy.jobs DEBUG 2016-05-17 23:18:50,308 (2) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-05-17 23:18:50,347 Job [2] queued (70.757 ms) +galaxy.jobs.handler INFO 2016-05-17 23:18:50,381 (2) Job dispatched +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:50,428 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:50,618 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.util.object_wrapper WARNING 2016-05-17 23:18:50,780 Unable to create dynamic subclass for <type 'instance'>, None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases +galaxy.tools.deps DEBUG 2016-05-17 23:18:50,790 Building dependency shell command for dependency 'r-snow' +galaxy.tools.deps DEBUG 2016-05-17 23:18:50,790 Find dependency r-snow version 0.4_1 +galaxy.tools.deps DEBUG 2016-05-17 23:18:51,402 Resolver conda returned <galaxy.tools.deps.resolvers.conda.CondaDepenency object at 0x7f6f8c1951d0> (isnull? False) +galaxy.tools.deps DEBUG 2016-05-17 23:18:51,403 Building dependency shell command for dependency 'r-probmetab' +galaxy.tools.deps DEBUG 2016-05-17 23:18:51,403 Find dependency r-probmetab version 1.1 +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:51,424 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:51,553 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.tools.deps DEBUG 2016-05-17 23:18:51,860 Resolver conda returned <galaxy.tools.deps.resolvers.conda.CondaDepenency object at 0x7f6f80269150> (isnull? False) +galaxy.tools.deps DEBUG 2016-05-17 23:18:51,860 Building dependency shell command for dependency 'r-batch' +galaxy.tools.deps DEBUG 2016-05-17 23:18:51,860 Find dependency r-batch version 1.1_4 +galaxy.tools.deps DEBUG 2016-05-17 23:18:52,081 Resolver conda returned <galaxy.tools.deps.resolvers.conda.CondaDepenency object at 0x7f6f8c1ab9d0> (isnull? False) +galaxy.jobs.command_factory INFO 2016-05-17 23:18:52,429 Built script [/tmp/tmpw4QiHm/job_working_directory/000/2/tool_script.sh] for tool command[[ "$CONDA_DEFAULT_ENV" = "/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env" ] || . /tmp/mc/bin/activate '/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env" ] || . /tmp/mc/bin/activate '/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env" ] || . /tmp/mc/bin/activate '/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env' 2>&1 ; LANG=C Rscript /projet/fr2424/sib/lecorguille/script/git/w4m/probmetab/galaxy/probmetab/probmetab.r mode_acquisition one xa /tmp/tmpw4QiHm/files/000/dataset_1.dat allowMiss TRUE html TRUE kegg_db KEGG ppm_tol 8 opt cor corths 0.75 corprob 0.8 pcorprob 0.8 prob count] +galaxy.tools.deps DEBUG 2016-05-17 23:18:53,207 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-05-17 23:18:53,207 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-05-17 23:18:53,208 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps DEBUG 2016-05-17 23:18:53,208 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps WARNING 2016-05-17 23:18:53,208 Failed to resolve dependency on 'samtools', ignoring +galaxy.jobs.runners DEBUG 2016-05-17 23:18:53,214 (2) command is: /tmp/tmpw4QiHm/job_working_directory/000/2/tool_script.sh; return_code=$?; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/AnalysisExample.html ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/AnalysisExample.html /tmp/tmpw4QiHm/files/000/dataset_2.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.tsv ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.tsv /tmp/tmpw4QiHm/files/000/dataset_3.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.zip ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.zip /tmp/tmpw4QiHm/files/000/dataset_4.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/sif.tsv ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/sif.tsv /tmp/tmpw4QiHm/files/000/dataset_5.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/probmetab.log ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/probmetab.log /tmp/tmpw4QiHm/files/000/dataset_6.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/variableMetadata.tsv ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/variableMetadata.tsv /tmp/tmpw4QiHm/files/000/dataset_7.dat ; fi; python "/tmp/tmpw4QiHm/job_working_directory/000/2/set_metadata_XTlz4J.py" "/tmp/tmpw4QiHm/tmp/tmpguw7h9" "/tmp/tmpw4QiHm/job_working_directory/000/2/galaxy.json" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_O7CAaw,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_MzQqwc,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_PaiB7e,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_Df5ACF,/tmp/tmpw4QiHm/files/000/dataset_2.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_H8F9z2" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_uTb9hi,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_ONUiky,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_xL3tZ_,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_KsHKNe,/tmp/tmpw4QiHm/files/000/dataset_3.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_ZFV3uC" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_xm7tlX,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_K8G_Qw,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_OnemTd,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4__WUZpk,/tmp/tmpw4QiHm/files/000/dataset_4.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_HYDXjN" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_EbwHj1,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_g1oZ1b,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_5sHnWe,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_nBtQCJ,/tmp/tmpw4QiHm/files/000/dataset_5.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_S1i0u0" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_6_0zrEpr,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_6_lMnxjA,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_6_6qIrJK,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_6_KkwfbW,/tmp/tmpw4QiHm/files/000/dataset_6.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_6_t_V9RY" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_7_ZOZSG9,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_7_IAS6VG,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_7_0m0j0a,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_7_I5kg2s,/tmp/tmpw4QiHm/files/000/dataset_7.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_7_9dCZcu" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-05-17 23:18:53,228 (2) executing job script: /tmp/tmpw4QiHm/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs DEBUG 2016-05-17 23:18:53,240 (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:53,472 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:53,597 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:18:56,803 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:18:56,913 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:19:03,322 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:19:03,438 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:19:16,254 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:19:16,370 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:19:41,999 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:19:42,111 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:20:33,364 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:20:33,475 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:22:15,978 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:22:16,097 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:25:40,999 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:25:41,110 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.jobs.runners.local DEBUG 2016-05-17 23:28:46,758 execution finished: /tmp/tmpw4QiHm/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs.output_checker INFO 2016-05-17 23:28:46,794 Job 2: Fatal error: Exit code 1 () +galaxy.jobs.output_checker DEBUG 2016-05-17 23:28:46,794 Tool exit code indicates an error, failing job. +galaxy.jobs DEBUG 2016-05-17 23:28:46,842 (2) setting dataset 2 state to ERROR +galaxy.jobs DEBUG 2016-05-17 23:28:46,872 (2) setting dataset 3 state to ERROR +galaxy.jobs DEBUG 2016-05-17 23:28:46,917 (2) setting dataset 4 state to ERROR +galaxy.jobs DEBUG 2016-05-17 23:28:46,947 (2) setting dataset 5 state to ERROR +galaxy.jobs DEBUG 2016-05-17 23:28:46,976 (2) setting dataset 6 state to ERROR +galaxy.jobs DEBUG 2016-05-17 23:28:47,006 (2) setting dataset 7 state to ERROR +galaxy.jobs DEBUG 2016-05-17 23:28:47,319 job 2 ended (finish() executed in (561.059 ms)) +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:30,813 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:30,922 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:30,924 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:30,966 "GET /api/histories/2891970512fa2d5a/contents?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:30,968 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,101 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,103 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,186 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,188 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,315 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,317 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,403 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,405 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,532 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,534 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,649 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,652 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,778 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,780 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,866 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:31,868 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:31,996 "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,001 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,089 "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,091 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,218 "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,219 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,310 "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,312 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,430 "GET /api/jobs/5729865256bc2525?full=true&key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,432 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,543 "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,545 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,588 "GET /api/histories/2891970512fa2d5a/contents?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,590 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,763 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,765 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:32,850 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:32,852 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,217 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,219 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,304 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,305 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,430 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,432 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,515 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,517 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,642 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,644 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,752 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,754 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,878 "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,879 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:33,966 "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:33,968 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:34,098 "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-05-17 23:32:34,100 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-05-17 23:32:34,195 "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +ERROR + +====================================================================== +ERROR: ProbMetab Tool ( Probmetab ) > Test-1 +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 133, in run + self.runTest(result) + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 151, in runTest + test(result) + File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 391, in __call__ + return self.run(*args, **kwds) + File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 331, in run + result.addFailure(self, sys.exc_info()) + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/proxy.py", line 146, in addFailure + plugins.addFailure(self.test, err) + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 99, in __call__ + return self.call(*arg, **kw) + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 167, in simple + result = meth(*arg, **kw) + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 93, in addFailure + self.print_test( 'failure', test, '\n'.join( traceback.format_exception( *error ) ) ) + File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 67, in print_test + print >> f.file, "<div id='capture_%d' style='display: none'><pre class='capture'>%s</pre></div>" % ( f.counter, cgi.escape( test.capturedOutput ) ) +UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 477: ordinal not in range(128) +-------------------- >> begin captured logging << -------------------- +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.tools: DEBUG: Validated and populated state for tool request (12.441 ms) +galaxy.tools.actions.upload: DEBUG: Persisted uploads (16.736 ms) +galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (255.374 ms) +galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 +galaxy.tools.actions.upload: DEBUG: Created upload job (142.419 ms) +galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (414.938 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (446.076 ms) +requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpw4QiHm/job_working_directory/000/1 +galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner +galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: Job [1] queued (103.400 ms) +galaxy.jobs.handler: INFO: (1) Job dispatched +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools' +galaxy.tools.deps: DEBUG: Find dependency samtools version None +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory: INFO: Built script [/tmp/tmpw4QiHm/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/tmpw4QiHm/galaxy-dev/tools/data_source/upload.py /tmp/tmpw4QiHm/galaxy-dev /tmp/tmpw4QiHm/tmp/tmpguw7h9 /tmp/tmpw4QiHm/tmp/tmprRgOLi 1:/tmp/tmpw4QiHm/job_working_directory/000/1/dataset_1_files:/tmp/tmpw4QiHm/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools' +galaxy.tools.deps: DEBUG: Find dependency samtools version None +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +galaxy.jobs.runners: DEBUG: (1) command is: /tmp/tmpw4QiHm/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/tmpw4QiHm/job_working_directory/000/1/set_metadata_uAINzL.py" "/tmp/tmpw4QiHm/tmp/tmpguw7h9" "/tmp/tmpw4QiHm/job_working_directory/000/1/galaxy.json" "/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1__6F4ZW,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_IAQkOq,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_wdkcNz,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_Fx0LLf,/tmp/tmpw4QiHm/files/000/dataset_1.dat,/tmp/tmpw4QiHm/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_FiInlP" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmpw4QiHm/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpw4QiHm/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1 +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.tools: DEBUG: Validated and populated state for tool request (73.065 ms) +galaxy.jobs: DEBUG: job 1 ended (finish() executed in (614.591 ms)) +galaxy.tools.actions: INFO: Handled output (76.304 ms) +galaxy.tools.actions: INFO: Handled output (43.535 ms) +galaxy.tools.actions: INFO: Handled output (44.088 ms) +galaxy.tools.actions: INFO: Handled output (51.731 ms) +galaxy.tools.actions: INFO: Handled output (51.534 ms) +galaxy.tools.actions: INFO: Handled output (138.001 ms) +galaxy.tools.actions: INFO: Verified access to datasets (5.855 ms) +galaxy.tools.execute: DEBUG: Tool [Probmetab] created job [2] (536.500 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (572.932 ms) +requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmpw4QiHm/job_working_directory/000/2 +galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner +galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) +galaxy.jobs.runners: DEBUG: Job [2] queued (70.757 ms) +galaxy.jobs.handler: INFO: (2) Job dispatched +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.util.object_wrapper: WARNING: Unable to create dynamic subclass for <type 'instance'>, None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases +galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-snow' +galaxy.tools.deps: DEBUG: Find dependency r-snow version 0.4_1 +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.conda.CondaDepenency object at 0x7f6f8c1951d0> (isnull? False) +galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-probmetab' +galaxy.tools.deps: DEBUG: Find dependency r-probmetab version 1.1 +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.conda.CondaDepenency object at 0x7f6f80269150> (isnull? False) +galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-batch' +galaxy.tools.deps: DEBUG: Find dependency r-batch version 1.1_4 +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.conda.CondaDepenency object at 0x7f6f8c1ab9d0> (isnull? False) +galaxy.jobs.command_factory: INFO: Built script [/tmp/tmpw4QiHm/job_working_directory/000/2/tool_script.sh] for tool command[[ "$CONDA_DEFAULT_ENV" = "/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env" ] || . /tmp/mc/bin/activate '/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env" ] || . /tmp/mc/bin/activate '/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env' 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env" ] || . /tmp/mc/bin/activate '/tmp/tmpw4QiHm/job_working_directory/000/2/conda-env' 2>&1 ; LANG=C Rscript /projet/fr2424/sib/lecorguille/script/git/w4m/probmetab/galaxy/probmetab/probmetab.r mode_acquisition one xa /tmp/tmpw4QiHm/files/000/dataset_1.dat allowMiss TRUE html TRUE kegg_db KEGG ppm_tol 8 opt cor corths 0.75 corprob 0.8 pcorprob 0.8 prob count] +galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools' +galaxy.tools.deps: DEBUG: Find dependency samtools version None +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x4455f50> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +galaxy.jobs.runners: DEBUG: (2) command is: /tmp/tmpw4QiHm/job_working_directory/000/2/tool_script.sh; return_code=$?; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/AnalysisExample.html ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/AnalysisExample.html /tmp/tmpw4QiHm/files/000/dataset_2.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.tsv ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.tsv /tmp/tmpw4QiHm/files/000/dataset_3.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.zip ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/Analysis_Report.zip /tmp/tmpw4QiHm/files/000/dataset_4.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/sif.tsv ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/sif.tsv /tmp/tmpw4QiHm/files/000/dataset_5.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/probmetab.log ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/probmetab.log /tmp/tmpw4QiHm/files/000/dataset_6.dat ; fi; if [ -f /tmp/tmpw4QiHm/job_working_directory/000/2/variableMetadata.tsv ] ; then cp /tmp/tmpw4QiHm/job_working_directory/000/2/variableMetadata.tsv /tmp/tmpw4QiHm/files/000/dataset_7.dat ; fi; python "/tmp/tmpw4QiHm/job_working_directory/000/2/set_metadata_XTlz4J.py" "/tmp/tmpw4QiHm/tmp/tmpguw7h9" "/tmp/tmpw4QiHm/job_working_directory/000/2/galaxy.json" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_O7CAaw,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_MzQqwc,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_PaiB7e,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_Df5ACF,/tmp/tmpw4QiHm/files/000/dataset_2.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_H8F9z2" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_uTb9hi,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_ONUiky,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_xL3tZ_,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_KsHKNe,/tmp/tmpw4QiHm/files/000/dataset_3.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_ZFV3uC" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_xm7tlX,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_K8G_Qw,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_OnemTd,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4__WUZpk,/tmp/tmpw4QiHm/files/000/dataset_4.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_HYDXjN" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_EbwHj1,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_g1oZ1b,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_5sHnWe,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_nBtQCJ,/tmp/tmpw4QiHm/files/000/dataset_5.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_S1i0u0" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_6_0zrEpr,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_6_lMnxjA,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_6_6qIrJK,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_6_KkwfbW,/tmp/tmpw4QiHm/files/000/dataset_6.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_6_t_V9RY" "/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_7_ZOZSG9,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_7_IAS6VG,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_7_0m0j0a,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_7_I5kg2s,/tmp/tmpw4QiHm/files/000/dataset_7.dat,/tmp/tmpw4QiHm/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_7_9dCZcu" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmpw4QiHm/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpw4QiHm/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs.output_checker: INFO: Job 2: Fatal error: Exit code 1 () +galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job. +galaxy.jobs: DEBUG: (2) setting dataset 2 state to ERROR +galaxy.jobs: DEBUG: (2) setting dataset 3 state to ERROR +galaxy.jobs: DEBUG: (2) setting dataset 4 state to ERROR +galaxy.jobs: DEBUG: (2) setting dataset 5 state to ERROR +galaxy.jobs: DEBUG: (2) setting dataset 6 state to ERROR +galaxy.jobs: DEBUG: (2) setting dataset 7 state to ERROR +galaxy.jobs: DEBUG: job 2 ended (finish() executed in (561.059 ms)) +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?full=true&key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/683bc220e21425bb/provenance?key=b685f1065f44c8bc0c7eb81cc81fb45c HTTP/1.1" 200 None +--------------------- >> end captured logging << --------------------- + +---------------------------------------------------------------------- +XML: /tmp/tmpw4QiHm/xunit.xml +---------------------------------------------------------------------- +Ran 1 test in 830.558s + +FAILED (errors=1) +functional_tests.py INFO 2016-05-17 23:32:34,212 Shutting down +functional_tests.py INFO 2016-05-17 23:32:34,213 Shutting down embedded web server +functional_tests.py INFO 2016-05-17 23:32:34,215 Embedded web server stopped +functional_tests.py INFO 2016-05-17 23:32:34,215 Shutting down app +galaxy.jobs.handler INFO 2016-05-17 23:32:34,215 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-05-17 23:32:34,215 job handler queue stopped +galaxy.jobs.runners INFO 2016-05-17 23:32:34,215 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-05-17 23:32:34,215 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-05-17 23:32:34,216 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-05-17 23:32:34,216 job handler stop queue stopped +functional_tests.py INFO 2016-05-17 23:32:34,216 Embedded Universe application stopped +functional_tests.py INFO 2016-05-17 23:32:34,216 Cleaning up temporary files in /tmp/tmp_QwDNn/tmpbNtbsc +galaxy.jobs.handler INFO 2016-05-17 23:32:35,102 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-05-17 23:32:35,102 job handler queue stopped +galaxy.jobs.runners INFO 2016-05-17 23:32:35,102 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-05-17 23:32:35,102 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-05-17 23:32:35,102 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-05-17 23:32:35,103 job handler stop queue stopped +cp: cannot stat `/tmp/tmpw4QiHm/jobfiles/*': No such file or directory +There were problems with 2 test(s) - out of 2 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/probmetab/galaxy/probmetab/tool_test_output.html for detailed breakdown. +Probmetab[0]: failed +Probmetab[0]: failed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,5 @@ + +# -- Use of conda dependencies +planemo conda_init --conda_prefix /tmp/mc +planemo conda_install --conda_prefix /tmp/mc . +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/probmetab.r Tue May 24 11:17:59 2016 -0400 @@ -0,0 +1,106 @@ +#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file +# probmetab.r version="1.0.0" +# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr + + +# ----- LOG ----- +log_file=file("probmetab.log", open = "wt") +sink(log_file) +sink(log_file, type = "out") + +# ----- PACKAGE ----- +cat("\tPACKAGE INFO\n") +pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab") +for(p in pkgs) { + suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) + cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") +} + +source_local <- function(fname){ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} +cat("\n\n") +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") +listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') + + +# ----- PROCESSING INFILE ----- +cat("\tINFILE PROCESSING INFO\n") + +# ----- INFILE PROCESSING ----- + +if(listArguments[["mode_acquisition"]]=="one") { + load(listArguments[["xa"]]) + #Unzip the chromatograms file for plotting EIC pour the HTML file + if(exists("zipfile")) + { + if (zipfile!=""){ + directory=unzip(zipfile) + } + } + if (!exists("xa")) { + xa=xsAnnotate_object + } + source_local("lib.r") + if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa); + +} else if(listArguments[["inputs_mode"]]=="two"){ + load(listArguments[["image_pos"]]) + #Unzip the chromatograms file for plotting EIC pour the HTML file + if(exists("zipfile")) { + if (zipfile!=""){ + directory=unzip(zipfile) + } + } + if (!exists("xa")) { + xa=xsAnnotate_object + } + xaP=xa + source_local("lib.r") + if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa) + else variableMetadataP=variableMetadata + + + load(listArguments[["image_neg"]]) + #Unzip the chromatograms file for plotting EIC pour the HTML file + if(exists("zipfile")) { + + if (zipfile!=""){ + directory=unzip(zipfile) + } + } + if (!exists("xa")) { + xa=xsAnnotate_object + } + xaN=xa + source_local("lib.r") + + if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa) + else variableMetadataN=variableMetadata +} + +print(directory) +print(dir(directory)) + +#Import the different functions +source_local("lib.r") +source_local("export.class.table-color-graph.R") + +# ----- PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + +if(listArguments[["mode_acquisition"]]=="one") { + results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments) +} else if(listArguments[["inputs_mode"]]=="two"){ + results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments) +} +#delete the parameters to avoid the passage to the next tool in .RData image +#rm(listArguments) +cat("\tDONE\n") +#saving R data in .Rdata file to save the variables used in the present tool +#save.image(paste("probmetab","RData",sep=".")) +