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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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Feather files readable but initializeScenic still throws error #149

Closed justin-malin closed 4 years ago

justin-malin commented 4 years ago

Hi,

I am having difficulty trying to initialize Scenic with the mm10 RcisTarget databases. This is despite the fact that i. the SHA256 sum matched the sum you gave, ii. the files can be read in using read_feather.

org="mgi" # or hgnc, or dmel dbDir='/Users/malinjl/Desktop/ATAC-Seq_data/TF-gene-correlation/scenicDB/' # RcisTarget databases location myDatasetTitle="SCENIC_output" # choose a name for your analysis dbs <- c('mm10refseq-r8010kb_up_and_down_tss.mc9nr.feather', 'mm10refseq-r80500bp_up_and_100bp_down_tss.mc9nr.feather')

scenicOptions <- initializeScenic(org=org, dbDir=dbDir, dbs=dbs, datasetTitle=myDatasetTitle, nCores=10) Motif databases selected: mm10refseq-r8010kb_up_and_down_tss.mc9nr.feather mm10refseq-r80500bp_up_and_100bp_down_tss.mc9nr.feather [1] "read failed on /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcisTarget/R/RcisTarget.rdb" [1] "read failed on /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcisTarget/R/RcisTarget.rdb" Warning messages: 1: In get0(oNam, envir = ns) : restarting interrupted promise evaluation 2: In get0(oNam, envir = ns) : restarting interrupted promise evaluation 3: 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: mm10refseq-r8010kb_up_and_down_tss.mc9nr.feather mm10refseq-r80500bp_up_and_100bp_down_tss.mc9nr.feather

As you can see below, the path is correct and the files readable: ('#' removed from copy-paste to aid formatting)

read_feather(paste0(dbDir, dbs[1])) A tibble: 24,453 x 24,131 features 0610005C13Rik 0610007P14Rik 0610009B22Rik 0610009L18Rik

1 jaspar_… 12011 8948 22962 13588 2 taipale… 18361 19752 22209 10950 3 taipale… 23295 12562 19815 21937 4 cisbp__… 19231 16187 22381 21534 5 scertf_… 18219 15933 20395 20282 6 hocomoc… 15230 8544 23123 20845 7 taipale… 17751 13108 22545 11472 8 transfa… 18235 16368 23446 22879 9 transfa… 22454 18989 23410 11805 10 transfa… 14753 15838 22823 20386 … with 24,443 more rows, and 24,126 more variables: `0610009O20Rik` , `0610010F05Rik` , `0610010K14Rik` , `0610012G03Rik` , `0610030E20Rik` , `0610031O16Rik` , `0610037L13Rik` , `0610038B21Rik` , `0610039H22Rik` , `0610039K10Rik` , …

Is there something that I am missing or doing incorrectly? I can provide more information as needed.

Thank you,

Justin

justin-malin commented 4 years ago

Somehow, just restarting Rstudio fixed the problem. It now initializes without an error.