Loading Feather Datasets from Tutorial

[AAA-3]

Hello -

I am new to bioinformatics and am going through the SCENIC tutorial. I am having trouble loading the databases. Here is my R code:

dbFiles <- c("/home/ali/Dokumente/R Practise/E14.5_Auswertung/WT_KO/Symposium+mit denen wird weitergearbeitet/SCENIC/cisTarget_databases",
             "/home/ali/Dokumente/R Practise/E14.5_Auswertung/WT_KO/Symposium+mit denen wird weitergearbeitet/SCENIC/cisTarget_databases")
org <- "mgi"
dbDir <- dbFiles
myDatasetTitle <- "SCENIC example on Mouse brain" # choose a name for your analysis
data(defaultDbNames)
dbs <- defaultDbNames[[org]]
scenicOptions <- initializeScenic(org=org, dbDir=dbDir, dbs=dbs, datasetTitle=myDatasetTitle, nCores=10) 

This is the Error message:

Motif databases selected: 
  mm9-500bp-upstream-7species.mc9nr.feather 
  mm9-tss-centered-10kb-7species.mc9nr.feather
[1] "Expected string vector of length 1"
[1] "Expected string vector of length 1"
Warning messages:
1: In initializeScenic(org = org, dbDir = dbDir, dbs = dbs, datasetTitle = myDatasetTitle,  :
  It was not possible to load the following databses; check whether they are downloaded correctly: 
mm9-500bp-upstream-7species.mc9nr.feather
mm9-tss-centered-10kb-7species.mc9nr.feather
2: In RcisTarget::importRankings(dbFile, columns = rnktype) :
  The following columns are missing from the database: features
3: In RcisTarget::importRankings(dbFile, columns = rnktype) :
  The following columns are missing from the database: features
4: In RcisTarget::importRankings(dbFile, columns = rnktype) :
  The following columns are missing from the database: features
5: In RcisTarget::importRankings(dbFile, columns = rnktype) :
  The following columns are missing from the database: features

R Session Info:

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SCopeLoomR_0.11.0  SCENIC_1.2.4       viridis_0.5.1      viridisLite_0.3.0  caTools_1.18.2     Cairo_1.5-12.2    
 [7] SeuratObject_4.0.0 Seurat_4.0.1       RcisTarget_1.10.0  AUCell_1.12.0      GENIE3_1.12.0     

[AAA-3]

Trying using the URL provided on the SCENIC Introduction and Set Up vignette:

Code:

dbFiles <- c("https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-500bp-upstream-7species.mc9nr.feather",
             "https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-7species.mc9nr.feather")
# mc9nr: Motif collection version 9: 24k motifs
org <- "mgi"
dbDir <- dbFiles
myDatasetTitle <- "SCENIC example on Mouse brain" # choose a name for your analysis
data(defaultDbNames)
dbs <- defaultDbNames[[org]]
scenicOptions <- initializeScenic(org=org, dbDir=dbDir, dbs=dbs, datasetTitle=myDatasetTitle, nCores=10) 

Also tried:

dbFiles <- c("https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-500bp-upstream-7species.mc9nr.feather",
             "https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-7species.mc9nr.feather")
# mc9nr: Motif collection version 9: 24k motifs

# dir.create("cisTarget_databases"); setwd("cisTarget_databases") # if needed
for(featherURL in dbFiles)
{
  download.file(featherURL, destfile=basename(featherURL)) # saved in current dir
}

Both received the same error:

Error in initializeScenic(org = org, dbDir = dbDir, dbs = dbs, datasetTitle = myDatasetTitle,  : 
  The following RcisTarget databases were not found: 
- https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-500bp-upstream-7species.mc9nr.feather/mm9-500bp-upstream-7species.mc9nr.feather 
- https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-7species.mc9nr.feather/mm9-500bp-upstream-7species.mc9nr.feather 
- https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-500bp-upstream-7species.mc9nr.feather/mm9-tss-centered-10kb-7species.mc9nr.feather 
- https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-7species.mc9nr.feather/mm9-tss-centered-10kb-7species.mc9nr.feather
Make sure the arguments 'dbDir' and 'dbs' are correct.

[AAA-3]

Have also attempted the following: https://github.com/aertslab/SCENIC/issues/43#issuecomment-820178705