Motif Database Error When Running Example Code

[pagarwal14]

Hi, I am new to SCENIC and installed it following the instructions on the github site. When I am try to run the example code I got the error Error in initializeScenic(org = org, dbDir = dbDir, dbs = dbs, datasetTitle = myDatasetTitle, : The following RcisTarget databases were not found:

• cisTarget_databases/mm9-500bp-upstream-7species.mc9nr.feather
• cisTarget_databases/mm9-tss-centered-10kb-7species.mc9nr.feather Then I realized the name of the database file that I downloaded is different: mm9-500bp-upstream-7species.mc9nr.genes_vs_motifs.rankings.feather mm9-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather So I renamed these files to the names in the error message. Now I am getting the following error:

scenicOptions <- initializeScenic(org=org, dbDir=dbDir, dbs=dbs, datasetTitle=myDatasetTitle, nCores=10) Motif databases selected: mm9-500bp-upstream-7species.mc9nr.feather mm9-tss-centered-10kb-7species.mc9nr.feather [1] "Invalid: Not an Arrow file" [1] "The index column 'features' is not available in the file." Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'getRanking': Invalid: Not an Arrow file In addition: Warning message: 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

My package versions are: SCENIC_1.3.1 SCopeLoomR_0.13.0 RcisTarget_1.14.0 AUCell_1.16.0

Please let me know which are the correct database files and how to obtain them. Thanks Pankaj

[AritaZ-hang]

I've occurred the same problem, and I find the old version .feather database is actually stored here: https://resources.aertslab.org/cistarget/databases/old/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/ May it be helpful to those who want to run this procedure