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.
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.