Error in running initializeScenic()

[mmaiensc]

Hi,

I'm trying to run initializeScenic() in R using the hg38 database (from https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gene_based/hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather) as follows:

dbDir = "/mnt/store3/clustcrilab/reference/pathways/SCENIC"
org = "hgnc"
dbName = "hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather"
scenicOptions = initializeScenic(org="hgnc",dbDir=dbDir, dbs=dbName)

And getting this error:

Motif databases selected: 
  hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather
[1] "The index column 'features' is not available in the file."
Using the column 'A1BG' as feature index for the ranking database.
Error: Can't extract columns that don't exist.
x Column `features` doesn't exist.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning messages:
1: In initializeScenic(org = "hgnc", dbDir = dbDir, dbs = dbName) :
  It was not possible to load the following databses; check whether they are downloaded correctly: 
hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather
2: In RcisTarget::importRankings(dbFile, columns = rnktype) :
  The following columns are missing from the database: features

I'm not sure if I'm specifying these inputs incorrectly, or if this is an error with an incomplete file. I was unable to find the sha256sum.txt file on the databases page to validate: this link returns a 404 error –https://resources.aertslab.org/cistarget/databases/sha256sum.txt. This is the sha256 checksum of the download that I have:

50bd3a2e0da17bf74ad31b1a2f284ebbacfad700a07a540a7a1d3db5e185eaac hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather

Otherwise, I'm not sure if the issue is with the version of arrow I have? Below is my session info from R:

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/linux-el7-x86_64-legacy/EasyBuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SCENIC_1.3.1

loaded via a namespace (and not attached):
 [1] ggrepel_0.9.1               Rcpp_1.0.7                 
 [3] lattice_0.20-45             png_0.1-7                  
 [5] Biostrings_2.62.0           assertthat_0.2.1           
 [7] utf8_1.2.2                  digest_0.6.28              
 [9] mime_0.12                   R6_2.5.1                   
[11] GenomeInfoDb_1.30.0         stats4_4.1.2               
[13] RSQLite_2.2.8               pillar_1.6.4               
[15] httr_1.4.2                  ggplot2_3.3.5              
[17] zlibbioc_1.40.0             rlang_0.4.12               
[19] data.table_1.14.2           annotate_1.72.0            
[21] blob_1.2.2                  S4Vectors_0.32.0           
[23] R.utils_2.11.0              R.oo_1.24.0                
[25] Matrix_1.3-4                AUCell_1.16.0              
[27] RCurl_1.98-1.5              bit_4.0.4                  
[29] munsell_0.5.0               shiny_1.7.1                
[31] DelayedArray_0.20.0         compiler_4.1.2             
[33] httpuv_1.6.3                pkgconfig_2.0.3            
[35] BiocGenerics_0.40.0         htmltools_0.5.2            
[37] tidyselect_1.1.1            SummarizedExperiment_1.24.0
[39] KEGGREST_1.34.0             tibble_3.1.5               
[41] GenomeInfoDbData_1.2.7      IRanges_2.28.0             
[43] matrixStats_0.61.0          XML_3.99-0.8               
[45] fansi_0.5.0                 dplyr_1.0.7                
[47] crayon_1.4.2                later_1.3.0                
[49] bitops_1.0-7                R.methodsS3_1.8.1          
[51] grid_4.1.2                  xtable_1.8-4               
[53] GSEABase_1.56.0             gtable_0.3.0               
[55] lifecycle_1.0.1             DBI_1.1.1                  
[57] magrittr_2.0.1              scales_1.1.1               
[59] graph_1.72.0                cachem_1.0.6               
[61] XVector_0.34.0              promises_1.2.0.1           
[63] generics_0.1.1              ellipsis_0.3.2             
[65] vctrs_0.3.8                 tools_4.1.2                
[67] bit64_4.0.5                 Biobase_2.54.0             
[69] glue_1.4.2                  purrr_0.3.4                
[71] MatrixGenerics_1.6.0        fastmap_1.1.0              
[73] AnnotationDbi_1.56.1        colorspace_2.0-2           
[75] GenomicRanges_1.46.0        memoise_2.0.0  

[ChenyuZhang97]

Hi, I encountered the same issue.
I tried to download the database from cisTarget databases - Feather v1 databases and solved the issue.
Hoping this could help you.

[LiuCanidk]

Hi, I encountered the same issue. I notice that you solve it by using mc9nr database, but it is not recommended by cisTarget since it is an older version (year 2017).

So I wonder if I can load the mcv10? I found the same error reporting the feature column not found.

[ChenyuZhang97]

Hi, probably we need to try pySCENIC. SCENIC (the R version) is no longer supported or updated. ////sad

[LiuCanidk]

Thanks for your reply, I would try pySCENIC then

…

---- Replied Message ---- | From | ***@***.***> | | Date | 10/22/2024 10:27 | | To | ***@***.***> | | Cc | ***@***.***>, ***@***.***> | | Subject | Re: [aertslab/SCENIC] Error in running initializeScenic() (Discussion #342) | Hi, probably we need to try pySCENIC. SCENIC (the R version) is no longer supported or updated. ////sad — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>