Hi.

When running the DEseq command, it proceeds to the "fitting model and testing" step where stalls longer than it should and then exits with this.

> dds < DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 2 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
LogicalList of length 24411
[["Xkr4"]] logical(0)
[["Rp1"]] logical(0)
[["Sox17"]] logical(0)
[["Mrpl15"]] logical(0)
[["Lypla1"]] logical(0)
[["Tcea1"]] logical(0)
[["Rgs20"]] logical(0)
[["Atp6v1h"]] logical(0)
[["Oprk1"]] logical(0)
[["Npbwr1"]] logical(0)
...
<24401 more elements>

It does not occur on all inputs. nor does it matter whether it is replacing outliers or not. Changing the design formula doesn't help either.

Any help would be greatly appreciated. 

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DESeq2 version 1.14.1

R version 3.3.2 (2016-10-31)

(answered by Wolfgang above)