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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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R is aborted when running initializeScenic #222

Open lucyu2668 opened 2 years ago

lucyu2668 commented 2 years ago

Hi, When I am running the code initializeScnic, the R is aborted. Is it due to the incomplete/corrupt of the dbfiles? How can I handle with it? Thanks~

Tomer9w commented 2 years ago

Not a member of the developer's team. I Downloaded the dbfiles through linux, then imported to my PC. worked. Hope It'll assisst you

s-aibar commented 2 years ago

[ Similar to issue #93 ]

Dear @lucyu2668 ,

Most of the issues when loading SCENIC are related to loading the databases: a) Due to incomplete downloads b) Due to inconsistent package versions (we had to change the interface to load the .feather files from package feather to arrow).

Could you confirm whether you can properly load the databases with these commands?

dbPath <-  "~/Downloads/cisTarget_databases/mm9-500bp-upstream-7species.mc9nr.feather" # Choose the appropriate database/location
SCENIC::dbLoadingAttempt(dbPath)

rnk <- RcisTarget::importRankings(dbPath, indexCol="features", columns=c("Sox10","Dlx1")) # you can load only a few genes to do tests faster
rnk

If the crash is indeed loading the databases:

  1. Please, make sure the mdsums of the databases match the ones from the server: https://resources.aertslab.org/cistarget/databases/sha256sum.txt

  2. Are you using the latest version of RcisTarget? (& what about feather and arrow?) i.e.

    packageVersion("RcisTarget")
packageVersion("arrow")
packageVersion("feather")
ghost commented 2 years ago

Dear @s-aibar,

I am having the same issue. I have made sure that the mediums of the databases match those on the sha256sum.txt and that I have the latest version of RcisTarget.

When I run the command to verify I can properly load the databases, my R aborts. Any suggestions? Thanks!

`> library(digest)

dbPath <- "/Users/francofelix/Desktop/feather/mm9-tss-centered-10kb-7species.mc9nr.feather" digest(dbPath, 'sha256', file=TRUE) [1] "ad7ee54883f5964c0e699e5c5bab08589eb0626599297085197cb6f80c5e12fc"

dbPath <- "/Users/francofelix/Desktop/feather/mm9-500bp-upstream-7species.mc9nr.feather" digest(dbPath, 'sha256', file=TRUE) [1] "bba21fb3b7e96ebfb97d31a59d661678973073b77b1c3e7a1bb2e49114a82425"

packageVersion("RcisTarget") [1] ‘1.14.0’ packageVersion("arrow") [1] ‘7.0.0’ packageVersion("feather") [1] ‘0.3.5’`

If I run either: dbPath <- "/Users/francofelix/Desktop/feather/mm9-tss-centered-10kb-7species.mc9nr.feather" # Choose the appropriate database/location SCENIC::dbLoadingAttempt(dbPath)

or

rnk <- RcisTarget::importRankings(dbPath, indexCol="features", columns=c("Sox10","Dlx1"))

My R session aborts.

If I try to run: scenicOptions <- initializeScenic(org="mgi", dbs = defaultDbNames[["mgi"]], dbDir="/Users/francofelix/Desktop/feather", nCores=4)

R will also abort.

Thanks!