goseQ Erorr based on Reference based rna seq tutorial

I want to get goseq done for my data but i saw this error, what this about ?
Warning message:
In pcls(G) : initial point very close to some inequality constraints
Loading required package: AnnotationDbi
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: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’:

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


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’:


Using manually entered categories.
Error in [.default(summary(map), , 1) : incorrect number of dimensions
Calls: runGoseq … goseq -> reversemapping -> [ -> [.table -> NextMethod

1 Like

This looks like an input format problem or disconnected input content. Try double-checking your inputs. Extra “whitespace”, empty lines, are the first item to check, and I’ve shared how to find those before with you directly (here & at the galaxy-bugs mailing list, with you and others).

A search by the tag “input” at Galaxy help will list out a lot of common format/content problems in posts where format as an issue, across tools, for others reading.

For you @amir, I would guess that “disconnected input content” is the root of the problem given the error message and since you already know how to confirm basic format. But if format checks not done yet, do that fist. After, much help is on the tool form regarding input dataset format/content, so review/compare your content versus the examples. There are columns of data between inputs and tool from entry data that ALL need to match up.

If that doesn’t work, preserve your testing of format/content in some history, that also contains the failed run, and send me a history share link with “objects shared” (direct message). I’ll have somewhat limited access for admin-only details at EU since I am not an admin at the EU server, but still may be able to review what may be going wrong. If not, can ping the EU server admins, or might suggest sending in a bug report via the UI (if you do that, be sure to leave all inputs undeteled and include a link to this post for context). You can also reply to this thread that you sent in the bug report, with the Public galaxy server URL included (to confirm where this is occurring).