Hi, I am performing several differential expression experiments with 1-factor, 2-conditions and 3 replicates per condition. I am currently getting a "....killed" message from R every time I run sleuth version sleuth/0.28.0-intel-2015b-R-3.2.1, right around the step so = sleuth_prep(s2c, ~condition)
so = sleuth_prep(s2c, ~condition) reading in kallisto results ...... normalizing est_counts 51842 targets passed the filter Killed
Does anyone know how to fix this? Or how to submit the R commands in a script so that I can submit it to our computer cluster, which has much more resources than the ones for the working window?
When I give the same commands, using the more recent sleuth/0.29.0-intel-2017a-R-3.4.0 instead, I get the following errors:
> so = sleuth_prep(s2c, ~condition) reading in kallisto results dropping unused factor levels ...... normalizing est_counts 51842 targets passed the filter normalizing tpm merging in metadata summarizing bootstraps ......Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, : HDF5. Dataset. Read failed. Error in order(indices) : unimplemented type 'list' in 'orderVector1'
Does anyone know what's going on? The most annoying thing is that, a few weeks back, this was working, which could mean resources are more scarse now, or something got updated maybe...? Any tips are welcome. Please note that I am a total R newb