DESEQ2 failing at http://usegalaxy.org

[jennaj]

Update2: Might be actual. Other tools show this symptom.

Tool

toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3

Error

Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Error in row.names<-.data.frame(*tmp*, value = value) : missing values in 'row.names' are not allowed Calls: rownames<- ... rownames<- -> row.names<- -> row.names<-.data.frame

All of the inputs look to be correct htseq_count files created within Galaxy (no spaces in gene names or in factor names).

Usage issue that someone recognizes or is this a bug? I can't check the version versus the tool shed right now, so am not sure if the version at http://usegalaxy.org is the most current or not. Will update when MTS online again.

[jennaj]

@bgruening The multi-select does seem to be at the root of the problem, or it is a good guess anyway. Other tools had problems distinguishing between multiple inputs in this form field. Example: https://github.com/galaxyproject/galaxy/issues/2989. Tested at usegalaxy.org, this is what DESEQ2 errors:

This might belong in the galaxyproject/galaxy repo instead. Lmk and I'll move it.

[natefoo]

deseq2 has been updated to version 2.1.8.4 if someone on the @galaxyproject/guac would like to test to see if the new version fixes it.

[jennaj]

testing, update once done

[jennaj]

Long error message, but perhaps there is a clue in here. The inputs seem fine from my checks. @galaxyproject/guac could one of you help to decode what is going wrong? Dependency issue (R?)

Dataset generation errors Dataset 131: DESeq2 result file on data 105, data 103, and others

Tool execution generated the following error message: Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

IQR, mad, xtabs

The following objects are masked from 'package:base':

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit

Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rcpp Loading required package: RcppArmadillo Warning messages: 1: replacing previous import by 'ggplot2::unit' when loading 'Hmisc' 2: replacing previous import by 'ggplot2::arrow' when loading 'Hmisc' 3: replacing previous import by 'scales::alpha' when loading 'Hmisc' Warning message: package 'getopt' was built under R version 3.3.1 Warning messages: 1: replacing previous import by 'ggplot2::unit' when loading 'Hmisc' 2: replacing previous import by 'ggplot2::arrow' when loading 'Hmisc' 3: replacing previous import by 'scales::alpha' when loading 'Hmisc' Warning message: package 'rjson' was built under R version 3.3.1 estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 116 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing Error in text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), : object 'h1' not found Calls: generateSpecificPlots -> text The tool produced the following additional output: discarding /galaxy/main/deps/_conda/bin from PATH prepending /galaxy-repl/main/jobdir/014/161/14161924/conda-env/bin to PATH

R version 3.2.2 (2015-08-14) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))

DESeq2 run information

sample table: HDMvsAM145 dataset_17589978.dat HDM dataset_17589980.dat HDM dataset_17589982.dat HDM dataset_17589984.dat HDM dataset_17589986.dat HDM dataset_17589988.dat HDM dataset_17589990.dat HDM dataset_17589997.dat HDM dataset_17590001.dat HDM dataset_17590003.dat HDM dataset_17590005.dat AM145 dataset_17590007.dat AM145 dataset_17590009.dat AM145 dataset_17590011.dat AM145 dataset_17590013.dat AM145 dataset_17590015.dat AM145 dataset_17590017.dat AM145 dataset_17590019.dat AM145 dataset_17590021.dat AM145 dataset_17590023.dat AM145

design formula: ~HDMvsAM145

primary factor: HDMvsAM145

---

20 samples with counts over 24421 genes using disperion fit type: parametric creating plots summary of results HDMvsAM145: AM145 vs HDM

out of 20330 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 3642, 18% LFC < 0 (down) : 3441, 17% outliers [1] : 0, 0% low counts [2] : 2742, 13% (mean count < 1) [1] see 'cooksCutoff' argument of ?results [2] see 'independentFiltering' argument of ?results

NULL

[jennaj]

Update: If "Visualising the analysis results" is set to "no", the tool runs. Could be the root issue or related. Shared history with @moheydarian in gitter

[devikaatgit]

Any updates/solutions for the issue? Its not just about multiple factors - the tools does not run even for just two basic factor levels. Tried running with the visualising the analysis results set to no but didnt get any results.

[jennaj]

@devikaatgit Hi Devika, thanks for the feedback and hope you are doing well!

The correction is still in progress. Much of the admin team is involved in training activities right now, but this is a priority too! Look for more updates next week. And you are correct - the tool can fail with even single factors. The original error was different than the most current.

If you are getting an error with visualization set to no, and are working at http://usegalaxy.org, could you send in a bug report? Would be helpful, thank you!

[bgruening]

@jennaj @natefoo there is a new DESeq2 update in the TS with conda package.

[jennaj]

ping @galaxyproject/guac FYI

[jennaj]

ping @natefoo the new version is ready. ETA for main update? https://toolshed.g2.bx.psu.edu/view/iuc/deseq2/4939397c4706

[natefoo]

@jennaj just updated it last night, restarted just now and the new version is available. Let me know if there are any problems.

[jennaj]

@natefoo Thanks, testing right now

Update - still getting errors. Might be data. Restarting another set.

Update2 - still failing

[jennaj]

Still failing

[jennaj]

The tool is working now for several test use cases - closing out, thanks everyone!