DEseq2 error; Job output not returned from cluster


I’m having trouble with DEseq2.
The error message im getting is; " Job output not returned from cluster"
What does it mean and how can I solve this?


Dear Sihae.
That could have different reasons. Please make an error report and look into the error message (click on the data and then on the excalamation mark, search for the standard output and standard error and post the text here). Here are few things that you can already check:

a) Run the tool again
b) Check if your count files have double header lines. Yes β†’ remove them
c) Check if all your files have the same number of rows and order of the rows, i.e., check if you used the same annotation for the counting.

That are still other things that might went wrong.

Have a good day and best wishes,

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Dear Flow

I run the test again. Once with File has header as β€˜Yes’ and once with β€˜No’.
In the header β€˜Yes’ case,

Tool Standard Output primary factor: space ---------------------
Tool Standard Error Error in data.frame(…, check.names = FALSE) : arguments imply differing number of rows: 20656, 20200, 20706, 20785, 21021, 20976 Calls: get_deseq_dataset … eval β†’ eval β†’ eval β†’ cbind β†’ cbind β†’ data.frame

and in header β€˜No’ case

Tool Standard Output primary factor: space ---------------------
Tool Standard Error Error in Ops.factor(a$V1, l[[1]]$V1) : level sets of factors are different Calls: get_deseq_dataset … DESeqDataSetFromHTSeqCount β†’ sapply β†’ sapply β†’ lapply β†’ FUN β†’ Ops.factor

Thanks for your help,

I suspect what is happening is that your factor level files are inconsistent in their size, which would cause the problem for both the header and non-header case. If you expand the datasets that you are using as inputs, are they listed as the same number of lines?

Dear astrov

As you said I checked the Input(StingTie gene counts) and found out that they had different number of lines. To fix that I switched reference file from Araport GTF file to TAIR10 GFF3 file and run StringTie. With different reference file they had all same number of lines as output.

But this time running DESeq2, I have got an error line like this

Tool Standard Error
Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character
Calls: get_deseq_dataset … DESeqDataSetFromHTSeqCount β†’ DESeqDataSetFromMatrix β†’ DESeqDataSet

Something should be in number instead its in character? What does it mean?
I searched to solve this error and found people encountered trying DESeq2 with R.
Im not sure how to solve that using Galaxy.


Dear @Sihae,
I believe that your count file is not in the correct format. Check again if you have additional header lines or you have entries in your count files that are named β€œNA” or β€œinf” or any string related entry.

If you still run into problems. Then please share your history with me.