Error in rule get_search_space: jobid: 11

[vcleon88]

I could not get the chromsizes.tsv data from human. It there anyone could help? thanks in advance.
scenicplus prepare_data download_genome_annotations --species "hsapiens" --genome_annotation_out_fname "/home/gu/scecis/plusout/genome_annotation2.tsv" --chromsizes_out_fname "/home/gu/scecis/plusout/chromsizes2.tsv"
/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/dataset.py:269: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
result = pd.read_csv(StringIO(response.text), sep='\t')
2024-10-24 15:28:14,135 Download gene annotation INFO Using genome: GRCh38.p14
Could not find IdList on https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=genome&term=GRCh38.p14
Returning gene annotation without subestting for assembled chromosomesand converting to UCSC style. Please make sure that the chromosome namesin the returned object match with the chromosome names in the scplus_obj.Chromosome sizes will not be returned
2024-10-24 15:28:14,140 SCENIC+ INFO Chrosomome sizes was not found, please provide this information manually.
2024-10-24 15:28:14,140 SCENIC+ INFO Saving genome annotation to: /home/gu/scecis/plusout/genome_annotation2.tsv

[SeppeDeWinter]

Hi @vcleon88

You can download this data manually from: https://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/

All the best,

Seppe