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ay-lab / mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
MIT License
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Mustache : IndexError: list index out of range #68

Open FCamera opened 3 weeks ago

FCamera commented 3 weeks ago

I am using Mustache to call loops on MICRO-C data mapped on human genome T2T version (CHM13/hs1) I run each chromosome individually with this code:

E.g. For chromosome 1 mustache -f -ch chr1 -r 5kb -st 0.7 -o <.tsv file>

It works for all the chromosomes except for chr9, chr15, chr16, chr21, and chrY. For these chromosomes I get the following error:

The distance limit is set to 2Mbp Reading contact map... 0 10000000 8000000 18000000 16000000 26000000 24000000 34000000 32000000 42000000 40000000 50000000 48000000 58000000 56000000 66000000 64000000 74000000 72000000 82000000 80000000 90000000 88000000 98000000 96000000 99753194 Traceback (most recent call last): File "/.conda/envs/mustache/bin/mustache", line 11, in sys.exit(main()) File "/.conda/envs/mustache/lib/python3.8/site-packages/mustache/mustache.py", line 1057, in main o = regulator(f, args.norm_method, CHRM_SIZE, args.outdir, File "/.conda/envs/mustache/lib/python3.8/site-packages/mustache/mustache.py", line 870, in regulator x, y, v = read_hic_file(f, norm_method, CHRM_SIZE, distance_in_bp, chromosome, chromosome2, res) File "/.conda/envs/mustache/lib/python3.8/site-packages/mustache/mustache.py", line 359, in read_hic_file x = np.array(result[0]) // res IndexError: list index out of range

I was wondering if I could get some help with this, Thanks a lot and regards, Francesco.

cemilcan98 commented 3 weeks ago

Hi Francesco,

The latest update on mustache.py should be taking care of this issue, can you check if you are using the latest code? Please let me know if that helps and works