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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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RcisTarget databases not found in initializeScenic() #163

Open dakotakatz opened 3 years ago

dakotakatz commented 3 years ago

I am struggling with the initializeScenic() command and keep getting the error that the RcisTarget databases were not found despite them existing at the file path I defined for dbDir. Is there another way to initialize Scenic?

or-lazarescu commented 3 years ago

same here: library(SCENIC) org="hgnc" # or mgi, or dmel dbDir="path/to/SCENIC/cisTarget_databases" # RcisTarget databases location myDatasetTitle="SCENIC example on adipose" # choose a name for your analysis data(defaultDbNames) dbs <- defaultDbNames[[org]] scenicOptions <- initializeScenic(org=org, dbDir=dbDir, dbs=dbs, datasetTitle=myDatasetTitle, nCores=1)

when running the above section i get this error: `Error in initializeScenic(org = org, dbDir = dbDir, dbs = dbs, datasetTitle = myDatasetTitle, : The following RcisTarget databases were not found:

these two files exist: list.files(dbDir) [1] " hg19-500bp-upstream-7species.mc9nr.feather" " hg19-tss-centered-10kb-7species.mc9nr.feather" [3] "desktop.ini"

s-aibar commented 3 years ago

Dear @or-lazarescu : In your code, the database names " hg19-500bp-upstream-7species.mc9nr.feather" include an extra space at the beginning. That could be the reason for them not to be found. Could you double-check that?

@dakotakatz : The main way to initialize SCENIC databases is through the initializeScenic function. You could also run the individual steps manually, but that will require more work... (see the detailed vignettes). We have just pushed a new version with some minor updates (including path.expand to the databases directory). That could solve your problem. If it doesn't, we will need some more information... Could you check whether this code works? 

library(SCENIC)
org <- "mgi" # or hgnc, or dmel
dbDir <- "cisTarget_databases" # RcisTarget databases location
dbDir <- path.expand(dbDir)

data(defaultDbNames)
dbs <- defaultDbNames[[org]]
dbs

lapply(dbs,function(x) file.exists(file.path(dbDir, x)))
or-lazarescu commented 3 years ago

thank you, I didn't notice the space!

meichendong commented 2 years ago

I had similar problem, and I tried your code above. I got this: > lapply(dbs,function(x) file.exists(file.path(dbDir, x))) $500bp` [1] FALSE

$10kb [1] FALSE`

Could you please suggest what could be wrong? Thanks, Meichen

fandi-2020 commented 2 years ago

I had similar problem, and I tried your code above. I got this: > lapply(dbs,function(x) file.exists(file.path(dbDir, x))) $500bp` [1] FALSE

$10kb [1] FALSE`

Could you please suggest what could be wrong? Thanks, Meichen

Hi I got the same issue here. Did you solve it ? Many thanks!

Di

Manman-Guo commented 1 year ago

I had similar problem, and I tried the code. I got this:

for(x in dbs) {

dbPath <- file.path(dbDir, x)

message(paste(dbPath, " --> Exists?:", file.exists(dbPath)))

}

cisTarget_databases/hg19-500bp-upstream-7species.mc9nr.feather --> Exists?: FALSE
cisTarget_databases/hg19-tss-centered-10kb-7species.mc9nr.feather --> Exists?: FALSE

In fact, I have manually downloaded the two files and put them in the cisTarget_databases. Could you please suggest what could be wrong? Thanks