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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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Error in hg19-500bp-upstream-10species.mc9nr.feather #315

Open daeun301 opened 1 year ago

daeun301 commented 1 year ago

Hi SCENIC team,

I'm running into the following error when I'm trying to run pyscenic ctx {ADJACENCIES_FNAME} {DBS_PARAM} :

"ValueError: "resources/hg19-500bp-upstream-10species.mc9nr.feather" is a cisTarget Feather database in Feather v1 format, which is not supported anymore. Convert them with "convert_cistarget_databases_v1_to_v2.py" (https://github.com/aertslab/create_cisTarget_databases/) to Feather v2 format."

I ran convert_cistarget_databases_v1_to_v2.py, but now am getting the following error:

"ValueError: cisTarget database filename "resources/hg19-500bp-upstream-10species-v2.mc9nr.feather" does not end with ".((motifs|tracks)vs(regions|genes)|(regions|genes)vs(motifs|tracks)).(scores|rankings).feather"."

The original feather files I downloaded was from https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/, and I haven't seen any new notes on feather files being named differently. Could you let me know how I can get around this error, and what name the feather files needs to be?

Thank you!

Best, Daeun

bkutlu commented 1 year ago

Hi Daeun, This issue can be resolved following the solution here:

https://github.com/aertslab/pySCENIC/issues/403