# Error while running GoSeq after cut the required columns and preparing the DE and Length files **URL:** \ **Category:** usegalaxy.org.au support\ **Tags:** workflow, tool-help, goseq\ **Created:** [May 1, 2026, 4:50pm UTC](https://help.galaxyproject.org/t/error-while-running-goseq-after-cut-the-required-columns-and-preparing-the-de-and-length-files/17701 "2026-05-01T16:50:35Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Haifa\_Hammad](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/haifa_hammad/32/6173_2.png) [@Haifa\_Hammad](https://help.galaxyproject.org/u/Haifa_Hammad)\ **Post date:** [May 1, 2026, 4:50pm UTC](https://help.galaxyproject.org/t/error-while-running-goseq-after-cut-the-required-columns-and-preparing-the-de-and-length-files/17701/1 "2026-05-01T16:50:35Z")
Hello, I have a problem while running the GoSeq tool. I used Advanced cut tool to obtaion the Geneid & True/False (Expression data) file and Geneid & Length file which were used in the GoSeq tool. the total number of rows and columns is ldentical and no (NA) in the file or spaces except tab space I tried many methods by downloading and doing it manually or using the provided cut tools to obtain the 2 files and to succeed in the GoSeq run however it always shows the following error. What can i do? and where is the error? Error: Warning message: In Sys.setlocale(“LC\_MESSAGES”, “en\_US.UTF-8”) : OS reports request to set locale to “en\_US.UTF-8” cannot be honored Warning messages: 1: In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L, : gam.fit3 algorithm did not converge 2: In pcls(G) : initial point very close to some inequality constraints Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:dplyr’: ``` combine, intersect, setdiff, union ``` The following objects are masked from ‘package:stats’: ``` IQR, mad, sd, var, xtabs ``` The following objects are masked from ‘package:base’: ``` Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min ``` 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: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:dplyr’: ``` first, rename ``` The following object is masked from ‘package:geneLenDataBase’: ``` unfactor ``` The following objects are masked from ‘package:base’: ``` I, expand.grid, unname ``` Attaching package: ‘IRanges’ The following objects are masked from ‘package:dplyr’: ``` collapse, desc, slice ``` Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:dplyr’: ``` select ``` Using manually entered categories. Error in `[.default`(summary(map), , 1) : incorrect number of dimensions Calls: run\_goseq … goseq → reversemapping → [ → [.table → NextMethod ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [May 1, 2026, 5:32pm UTC](https://help.galaxyproject.org/t/error-while-running-goseq-after-cut-the-required-columns-and-preparing-the-de-and-length-files/17701/2 "2026-05-01T17:32:19Z")
Welcome @Haifa_Hammad 🙂 Thanks for sharing the error details! Very helpful. This the part to pay attention to > Using manually entered categories > incorrect number of dimensions This usually means the issue is with the **category mapping file** , not the GeneID/True/False or GeneID/Length inputs. For GOseq, the category file should be very simple: **2 columns only** ```auto GeneID CategoryID ``` > gene1 GO:0008150 > gene1 GO:0003674 > gene2 GO:0009987 Common problems: - More than 2 columns - Missing tab separation - GeneIDs not matching your other two files exactly - File formatted as a matrix instead of a simple 2-column list Some prior discussions are here: - “Goseq: incorrect number of dimensions” [https://help.galaxyproject.org/t/goseq-incorrect-number-of-dimensions/12647](https://help.galaxyproject.org/t/goseq-incorrect-number-of-dimensions/12647) - “Using GOseq with a custom category input” [https://help.galaxyproject.org/t/using-goseq-with-a-custom-category-input/10770](https://help.galaxyproject.org/t/using-goseq-with-a-custom-category-input/10770) If you want to try to resolve it yourself with more of the text manipulation tools, we have some resources: > [@How to solve problems with data formats: GTN Data Manipulation Olympics tutorials!](https://help.galaxyproject.org/t/how-to-solve-problems-with-data-formats-gtn-data-manipulation-olympics-tutorials/14970/2): > > - [Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html) > - More → [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=olympics) (query=olympics) Or, you can generate a share link to your history and post that back in a reply, then unshare after we are done. - [FAQ: Sharing your History](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) Let’s start there and if you solve this, please let us know! I’ll watch for your reply. 🚀