Genomic region

[dzwzs]

Hi all, I'm running hicDifferentialTAD on TADs identified by hicFindTADs on my data. I've run into some tough issues and I'd love some help.

$ singularity exec ~/04.workspace/16.HIC/sifs/hicexplorer_20240327.sif hicDifferentialTAD  \
-tm ../Final/Csch.mcool::/resolutions/50000 \
-cm  ../Final/Dbra.mcool::/resolutions/50000 \
-td ./Csch__domains.bed \
-o Csch_vs_Dbra \
--mode all \
-p 0.01 \
-t 4 \
-mr all

ERROR:hicmatrix.lib.cool:Wrong chromosome format. Please check UCSC / ensembl notation.
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 121, in load
    matrix = cooler_file.matrix(balance=False, sparse=True, as_pixels=False).fetch(self.chrnameList[0]).tocsr()  # pylint: disable=E1136
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 149, in fetch
    i0, i1, j0, j1 = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 392, in _fetch
    region1 = parse_region(region, self._chromsizes)
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [49750000, 50850000)
ERROR:hicmatrix.lib.cool:Error: Genomic region out of bounds: [49750000, 50850000)
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 121, in load
    matrix = cooler_file.matrix(balance=False, sparse=True, as_pixels=False).fetch(self.chrnameList[0]).tocsr()  # pylint: disable=E1136
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 149, in fetch
    i0, i1, j0, j1 = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 392, in _fetch
    region1 = parse_region(region, self._chromsizes)
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [49750000, 50850000)
ERROR:hicmatrix.lib.cool:Wrong chromosome format. Please check UCSC / ensembl notation.
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 121, in load
    matrix = cooler_file.matrix(balance=False, sparse=True, as_pixels=False).fetch(self.chrnameList[0]).tocsr()  # pylint: disable=E1136
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 149, in fetch
    i0, i1, j0, j1 = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 392, in _fetch
    region1 = parse_region(region, self._chromsizes)
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [69800000, 71300000)
ERROR:hicmatrix.lib.cool:Error: Genomic region out of bounds: [69800000, 71300000)
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 121, in load
    matrix = cooler_file.matrix(balance=False, sparse=True, as_pixels=False).fetch(self.chrnameList[0]).tocsr()  # pylint: disable=E1136
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 149, in fetch
    i0, i1, j0, j1 = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 392, in _fetch
    region1 = parse_region(region, self._chromsizes)
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [69800000, 71300000)
ERROR:hicmatrix.lib.cool:Wrong chromosome format. Please check UCSC / ensembl notation.
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 121, in load
    matrix = cooler_file.matrix(balance=False, sparse=True, as_pixels=False).fetch(self.chrnameList[0]).tocsr()  # pylint: disable=E1136
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 149, in fetch
    i0, i1, j0, j1 = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 392, in _fetch
    region1 = parse_region(region, self._chromsizes)
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [41100000, 43950000)
ERROR:hicmatrix.lib.cool:Error: Genomic region out of bounds: [41100000, 43950000)
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 121, in load
    matrix = cooler_file.matrix(balance=False, sparse=True, as_pixels=False).fetch(self.chrnameList[0]).tocsr()  # pylint: disable=E1136
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 149, in fetch
    i0, i1, j0, j1 = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 392, in _fetch
    region1 = parse_region(region, self._chromsizes)
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [41100000, 43950000)
ERROR:hicexplorer.hicDifferentialTAD:Genomic region out of bounds: [41100000, 43950000)Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/hicexplorer/hicDifferentialTAD.py", line 133, in computeDifferentialTADs
    hic_matrix_control_inter_tad = hm.hiCMatrix(
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/HiCMatrix.py", line 54, in __init__
    matrixFileHandler_load = self.matrixFileHandler.load()
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/matrixFileHandler.py", line 52, in load
    return self.matrixFile.load()
  File "/opt/conda/lib/python3.10/site-packages/hicmatrix/lib/cool.py", line 155, in load
    cut_intervals_data_frame = cooler_file.bins().fetch(self.chrnameList[0])
  File "/opt/conda/lib/python3.10/site-packages/cooler/core/_selectors.py", line 115, in fetch
    lo, hi = self._fetch(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/cooler/api.py", line 268, in _fetch
    parse_region(region, self._chromsizes),
  File "/opt/conda/lib/python3.10/site-packages/cooler/util.py", line 178, in parse_region
    raise ValueError(f"Genomic region out of bounds: [{start}, {end})")
ValueError: Genomic region out of bounds: [41100000, 43950000)