aertslab / create_cisTarget_databases

Create cisTarget databases
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TypeError: write_feather() got an unexpected keyword argument 'compression' #23

Closed hcph closed 1 year ago

hcph commented 1 year ago

Hello, thank you for developing such powerful tool. I met a question that hard to solve, the command is as following: fasta_filename="test.fa" motifs_dir="motifs_cb_format" motifs_list_filename="motifs.lst" db_prefix="st" nbr_threads=20 cd /public/home/chaohe/create_cisTarget_databases

Score all motifs at once and create rankings

create_cistarget_motif_databases.py \ -f "${fasta_filename}" \ -M "${motifs_dir}" \ -m "${motifs_list_filename}" \ -o "${db_prefix}" \ -t "${nbr_threads}"

when running this, I would get one error: Scoring 530 motifs with Cluster-Buster took: 3.247628 seconds

Writing cisTarget regions vs motifs scores db: "st.motifs_vs_regions.scores.feather" Traceback (most recent call last): File "/public/home/chaohe/create_cisTarget_databases/create_cistarget_motif_databases.py", line 539, in main() File "/public/home/chaohe/create_cisTarget_databases/create_cistarget_motif_databases.py", line 490, in main write_db(ct_db=ct_scores_db_motifs_vs_regions_or_genes, db_prefix=db_prefix) File "/public/home/chaohe/create_cisTarget_databases/create_cistarget_motif_databases.py", line 480, in write_db version=2, File "/public/home/chaohe/create_cisTarget_databases/cistarget_db.py", line 1208, in write_db version=version, TypeError: write_feather() got an unexpected keyword argument 'compression'

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Could you please help me? Thank you very much!

hcph commented 1 year ago

This all about the environmental error of conda