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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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initializeScenic: getDbAnnotations error #356

Open hernandezvargash opened 1 year ago

hernandezvargash commented 1 year ago

Hi, I've been using SCENIC's R version in linux environment with success until last week, but now I get an error when trying to initialize (please see below). I used the same code and databases that worked earlier for me, so the issue must be somewhere else. Traceback stops after the 2nd step: getDbAnnotations(object) . I get the same error when using default RcisTarget databases, and this persists after updating my libraries (current versions: SCENIC 1.3.1, RcisTarget 1.17.0, GENIE3 1.20.0, AUCell 1.20.0). I couldn't find the same error in any earlier post. Did anybody find a similar error and can suggest a solution? Thanks for your help! Hector

This is my code: 

dbs <- c('500bp' = "mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather",
         '10kb' = "mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather")

scenicOptions <- initializeScenic(org= "mgi", 
                                  dbDir= "~/RcisTarget_databases", 
                                  dbs= dbs, 
                                  datasetTitle= "SCENIC", 
                                  nCores=12)

And the error:

_Motif databases selected: mm10refseq-r8010kb_up_and_down_tss.mc9nr.feather mm10refseq-r80500bp_up_and_100bp_downtss.mc9nr.feather Error in data(list = motifAnnotName, package = "RcisTarget", verbose = FALSE) : unused arguments (list = motifAnnotName, package = "RcisTarget", verbose = FALSE)

s-aibar commented 1 year ago

Dear @hernandezvargash ,

It seems you are using the very last version of RcisTarget and AUCell (just published on Nov 2). I have not updated SCENIC to work with those packages yet. I'll try to do it over the next days, but meanwhile it will be easier if you keep using the previous versions.

hernandezvargash commented 1 year ago

Thank you @s-aibar for the fast response. I'll go back to the previous versions and try again. The reason I updated was because of this error, but I may have missed something. I'll let you know if this works. Thanks!

hernandezvargash commented 1 year ago

Hello, My code is working now after downgrading like this: SCENIC : 1.1.2 RcisTarget : 1.16.0 AUCell : 1.18.1 I forgot to mention in my previous post that I also upgraded to R version 4.2.2, although the old packages seem to be working fine in this R version. Thanks again for your help!

hernandezvargash commented 1 year ago

I managed to pass the initializeScenic step, but now I get the same error at the runGenie3 step:

runGenie3(exprMat_filtered, scenicOptions)
Error in data(list = motifAnnotName, package = "RcisTarget", verbose = FALSE) : 
  unused arguments (list = motifAnnotName, package = "RcisTarget", verbose = FALSE)

GENIE3 version 1.18.0

hernandezvargash commented 1 year ago

this issue seems to be related with issue #334 runGenie3 seems to be working for me after following @joyduck indicationes here: https://github.com/aertslab/SCENIC/issues/334#issuecomment-1300654055 except this time I'm using the most recent versions of the mm10 databases:

dbs <- c('500bp' = "mm10_500bp_up_100bp_down_full_tx_clustered.genes_vs_motifs.rankings.feather",
         '10kb' = "mm10_10kbp_up_10kbp_down_full_tx_clustered.genes_vs_motifs.rankings.feather")
Polligator commented 1 year ago

I'm not sure if you should use their most recent database, it appears to me that the number of TFs in the new database is the same as the old one(mouse), probably the same set of TFs, not sure what has been updated, it might do not worth the time to mess around to use the new database. you might want to compare if the results generated by the old and new database are the same, I did not have time to do it yet. I also asked a question in the discussion #355 about this, has not get a reply yet, if the authors see this, could you please let me know? thanks very much and I'm looking forward to your answer.

Linnnnnn7 commented 9 months ago

I managed to pass the initializeScenic step, but now I get the same error at the runGenie3 step:

runGenie3(exprMat_filtered, scenicOptions)
Error in data(list = motifAnnotName, package = "RcisTarget", verbose = FALSE) : 
  unused arguments (list = motifAnnotName, package = "RcisTarget", verbose = FALSE)

GENIE3 version 1.18.0

Hi, I have the same error as yours and can not pass the "initializeScenic" step. How did you fix this?