Closed Sylviavictor closed 5 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
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"
the hic data you provide must have 5k BP resolution and be SCALE normalized
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