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broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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ABC with Hg38 #197

Closed Sylviavictor closed 5 months ago

Sylviavictor commented 6 months ago

Hi Authors, Thank you for your fantastic tool; however, I am now experiencing a problem while attempting to use HiC data for the Hg38 version of the genome.

This was the Command used: python ABC-Enhancer-Gene-Prediction/workflow/scripts/predict.py \ --enhancers GrCh38/ABC_output/K562/Neighborhoods/EnhancerList.txt \ --genes GrCh38/ABC_output/K562/Neighborhoods/GeneList.txt \ --hic_file GrCh38/input_data/Hic/4DNFITUOMFUQ.hic \ --chrom_sizes reference/chr_sizes \ --hic_resolution 5000 \ --cellType K562 \ --scale_hic_using_powerlaw \ --outdir GrCh38/ABC_output/K562/Predictions \ --accessibility_feature DHS \ --make_all_putative \ --chromosome chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrM

Traceback (most recent call last): File "ABC-Enhancer-Gene-Prediction/workflow/scripts/predict.py", line 303, in main() File "ABC-Enhancer-Gene-Prediction/workflow/scripts/predict.py", line 242, in main this_chr = make_predictions( File "ABC-Enhancer-Gene-Prediction/workflow/scripts/predictor.py", line 24, in make_predictions pred = add_powerlaw_to_predictions(pred, args, hic_gamma, hic_scale) File "ABC-Enhancer-Gene-Prediction/workflow/scripts/predictor.py", line 337, in add_powerlaw_to_predictions pred["powerlaw_contact"] = get_powerlaw_at_distance( File "ABC-Enhancer-Gene-Prediction/workflow/scripts/hic.py", line 295, in get_powerlaw_at_distance assert scale > 0 TypeError: '>' not supported between instances of 'NoneType' and 'int'

Hope you can help me with this Thanks, Sylvia

atancoder commented 6 months ago

Looks like you're not passing in the --hic_scale parameter to the function. I would recommend using Snakemake instead of running the commands manually. Snakemake will handle filling out all the required parameters for you

Sylviavictor commented 6 months ago

Thanks for your reply , I tried adding in the --hic_scale and I am getting a warning " File did not contain SCALE normalization vectors for one or both chromosomes at 5000 BP"

atancoder commented 6 months ago

the hic data you provide must have 5k BP resolution and be SCALE normalized