pyBHFDR can't find weight column

[wangzwYYDS]

pyBHFDR -O K562-MboI-BHFDR-loops.txt -p Ga.40000.a.cool::40000 -C 4 --pw 1 --ww 3

root INFO @ 10/08/23 15:58:09: Python Version: 3.6.15 root INFO @ 10/08/23 15:58:09:

ARGUMENT LIST:

Output file = K562-MboI-BHFDR-loops.txt

Cooler URI = Ga.40000.cool::40000

Chromosomes = ['4']

Peak window width = 1

Donut width = 3

Maximum donut width = 10

Significant Level = 0.05

Maximum Genomic distance = 2000000

Weight column name = weight

Number of Processes = 1

root INFO @ 10/08/23 15:58:10: Loading Hi-C data ... root INFO @ 10/08/23 15:58:10: Calling Peaks ... Traceback (most recent call last): File "/data/Software/miniconda3/envs/TADlib/bin/pyBHFDR", line 185, in run() File "/data/Software/miniconda3/envs/TADlib/bin/pyBHFDR", line 169, in run for key, pixel_table in results: File "/data/Software/miniconda3/envs/TADlib/bin/pyBHFDR", line 116, in worker cHeatMap = Lib.matrix(balance=args.clr_weight_name, sparse=True).fetch(key) File "/data/Software/miniconda3/envs/TADlib/lib/python3.6/site-packages/cooler/core/_selectors.py", line 150, in fetch return self._slice(self.field, i0, i1, j0, j1) File "/data/Software/miniconda3/envs/TADlib/lib/python3.6/site-packages/cooler/api.py", line 384, in _slice self._is_symm_upper, File "/data/Software/miniconda3/envs/TADlib/lib/python3.6/site-packages/cooler/api.py", line 710, in matrix + "calculate balancing weights or set balance=False." ValueError: No column 'bins/weight'found. Use cooler.balance_cooler to calculate balancing weights or set balance=False.

toCool

toCooler -O Ga.40000.a.cool -d datasets --chromsizes-file aa.leng --no-balance --nproc 1

root INFO @ 10/08/23 16:06:11: Python Version: 3.6.15 root INFO @ 10/08/23 16:06:11:

ARGUMENT LIST:

Output cooler path = Ga.40000.a.cool

Hi-C datasets = {40000: '/gpfs/Project/wangzw_Project/TDA_analysis/test/HiCPeaks/40K'}

Chromosomes = ['#', 'X']

Include trans-chromosomal data = False

Genome Assembly = None

Chromosome size file = aa.leng

Number of processes = 1

Log file name = tocooler.log

hicpeaks.utilities INFO @ 10/08/23 16:06:12: Read chromosome sizes from /gpfs/Project/wangzw_Project/TDA_analysis/test/HiCPeaks/aa.leng hicpeaks.utilities INFO @ 10/08/23 16:06:12: Done hicpeaks.utilities INFO @ 10/08/23 16:06:12: Extract and save data into cooler format for each resolution ... hicpeaks.utilities INFO @ 10/08/23 16:06:12: Current resolution: 40000bp hicpeaks.utilities INFO @ 10/08/23 16:06:12: Generate bin table ...

first, do toCooler convert txt file to cool file format .
then call peaks using pyBHFDR , has some error message . don't know how to solve it. thanks

[lanyunxin]

I have the same problem. Have you solved it

[lhqxinghun]

I have met the same problem. Can someone help me?

[lhqxinghun]

I have met the same problem. Can someone help me?

I have addressed this by setting the reference genome to hg19 instead of hg38 in toCooler, because I found that using hg38 may cause the matrix in cooler file not square.