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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Not able run load databases getting error #366

Closed luckysardar closed 1 year ago

luckysardar commented 1 year ago

<--

I trying use Scenic but with the below step I getting the erorr please anyone suggest is it version problem because my databses are okay and i have run some command mentiond in #222 ran without any errorr showed features

scenicOptions <- initializeScenic(org="mgi", dbDir=db_path , dbs = dbs, nCores=10) 

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Motif databases selected: 
  mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.genes_vs_motifs.rankings.feather 
  mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather
[1] "The index column 'features' is not available in the file."
[1] "The index column 'features' is not available in the file."
Using the column '0610005C13Rik' as feature index for the ranking database.
Error in `dplyr::pull()`:
! Can't extract columns that don't exist.
✖ Column `features` doesn't exist.
Run `rlang::last_error()` to see where the error occurred.
Warning messages:
1: In initializeScenic(org = "mgi", dbDir = db_path, dbs = dbs, nCores = 10) :
  It was not possible to load the following databses; check whether they are downloaded correctly: 
mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.genes_vs_motifs.rankings.feather
mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather
2: In RcisTarget::importRankings(dbFile, columns = rnktype) :
  The following columns are missing from the database: features

issue resolved with change the data base name #208