Question: "database or disk is full" error in enrichGO function for CHIPSeeker tutorial
0
gravatar for morten.rye
5 months ago by
morten.rye0
morten.rye0 wrote:

I am following the tutorial for CHIPSeeker at

https://hbctraining.github.io/Intro-to-ChIPseq/lessons/12_functional_analysis.html

Everything works fine, except when I run the enrichGO call to create an ego object. No matter what I do I get the following error:

ego <- enrichGO(gene = entrez,
+                 keyType = "ENTREZID",
+                 OrgDb = org.Mm.eg.db,
+                 ont = "CC",
+                 pAdjustMethod = "BH",
+                 qvalueCutoff = 0.05,
+                 readable = TRUE)
Error: database or disk is full

However, my disk is clearly not full (907 GB free), so something else must be going on. The KEGG analysis also described works perfectly. Appreciate any suggestions.

FYI: I am using a anaconda2 installation of R3.6.1 on an old ubuntu 12

ADD COMMENTlink modified 5 months ago • written 5 months ago by morten.rye0

However, my disk is clearly not full (907 GB free), so something else must be going on.

Many programs use temporary disks, which may be different from where you do data analysis. I suggest you check that a disk holding /tmp directory is not full.

ADD REPLYlink written 5 months ago by Mensur Dlakic6.9k
0
gravatar for morten.rye
5 months ago by
morten.rye0
morten.rye0 wrote:

Did not find the /tmp directory, but installed it again on a newer server (ubuntu 18), and this time it worked fine. So you may very well have been correct. Thanks!

ADD COMMENTlink written 5 months ago by morten.rye0

cd /tmp, this is the memory of your machine. If a tool spams that location with any temporary files then you have at some point a memory shortage.

ADD REPLYlink written 5 months ago by ATpoint40k
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