Question: kallisto + sleuth: no results
0
gravatar for stephanie.devos
20 months ago by
stephanie.devos0 wrote:

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

rna-seq kallisto sleuth R • 1.3k views
ADD COMMENTlink modified 3 months ago by gilbo10 • written 20 months ago by stephanie.devos0
1

The suspense is killing me, I get the impression that your post is incomplete.

ADD REPLYlink written 20 months ago by WouterDeCoster37k

so what do you think?

ADD REPLYlink written 19 months ago by stephanie.devos0
1

Can you paste the full code?

ADD REPLYlink written 20 months ago by Biojl1.6k

so what do you think?

ADD REPLYlink written 19 months ago by stephanie.devos0

Sure, here it is:

suppressMessages({
   library("sleuth")
 })
sample_id <- dir(file.path("..", "results_sleuthexample"))
sample_id
kal_dirs <- file.path("..", "results_sleuthexample", sample_id, "kallisto")
kal_dirs
s2c <- read.table(file.path("..", "metadata_sleuthexample", "hiseq_info.txt"), header = TRUE, stringsAsFactors=FALSE)
s2c <- dplyr::select(s2c, sample = run_accession, condition)
s2c
s2c <- dplyr::mutate(s2c, path = kal_dirs)
print(s2c)
so = sleuth_prep(s2c, ~condition)
ADD REPLYlink written 20 months ago by stephanie.devos0

Hi, Have you fixed the error "Error in order(indices) : unimplemented type 'list' in 'orderVector1'""?

ADD REPLYlink written 18 months ago by philgev210

Hi, no, any idea what it means (why do I get this error with the newer version of Sleuth and not with the old one??) or how I could fix it? As I said, R skills low at the moment, although I try to catch up. Thank you for any suggestion!

ADD REPLYlink modified 18 months ago • written 18 months ago by stephanie.devos0
1
gravatar for philgev2
18 months ago by
philgev210
philgev210 wrote:

Hi

I was running the code on Amazon EC2. It seems error is because of some broken parallel processing. When i re-run the code with parameter num_cores=2, code run without error.

Thanks Philge

ADD COMMENTlink written 18 months ago by philgev210
1
gravatar for gilbo
3 months ago by
gilbo10
gilbo10 wrote:

If anyone comes across this, when I encountered this error I realized I had forgotten to request enough memory from the cluster. I suspect that is also why when someone drops the number of cores it will fix the issue as well.

ADD COMMENTlink written 3 months ago by gilbo10
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