Error with hicFindTADs

[spiderzbh]

Welcome to the HiCExplorer GitHub repository! Before opening the issue please check that the following requirements are met :

• [x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below. Didn't find a similar issue.

• [x] Paste your HiCExplorer version (hicInfo --version) and your python version (python --version) below. hicInfo 3.7.2; Python 3.8.3.

• [x] Have you checked our documentation on hicexplorer.readthedocs.io? Yes.

• [x] Do you use conda to install HiCExplorer? Yes, I used conda to instal the software. (conda install hicexplorer -c bioconda -c conda-forge)

• [x] Do you use the latest HiCExplorer release? If not, please install it via a conda environment: conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge and activate the environment: conda activate hicexplorer. Retry your command. You can exit a conda environment via conda deactivate. To learn more about conda and environments, please consider the following documentation. The HiCExplorer is the latest version.

Retry your command, is it solved now? If not please continue with the following:

• [x] Paste the full HiCExplorer command that produces the issue below (ignore if you simply spotted the issue in the code/documentation). Command A: hicFindTADs -m GSE77565_FBP_IC-heatmap-chr-40k.hdf5 --outPrefix tmp --correctForMultipleTesting fdr Command B: hicFindTADs -m GSE77565_FBD_40K.h5 --outPrefix tmp --correctForMultipleTesting fdr

• [x] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation). Output from A: Traceback (most recent call last): File "/home/bz10/usr/miniconda3/bin/hicFindTADs", line 7, in main() File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicexplorer/hicFindTADs.py", line 1313, in main ft = HicFindTads(args.matrix, num_processors=args.numberOfProcessors, max_depth=args.maxDepth, File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicexplorer/hicFindTADs.py", line 375, in init self.set_matrix(matrix, pChromosomes) File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicexplorer/hicFindTADs.py", line 396, in set_matrix self.hic_ma = hm.hiCMatrix(pMatrix) File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicmatrix/HiCMatrix.py", line 59, in init raise Exception('Matrix failed to load: {}'.format(str(matrixFileHandler_load[1]))) Exception: Matrix failed to load: 'No cooler found at: GSE77565_FBP_IC-heatmap-chr-40k.hdf5.' Output from B: Traceback (most recent call last): File "/home/bz10/usr/miniconda3/bin/hicFindTADs", line 7, in main() File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicexplorer/hicFindTADs.py", line 1313, in main ft = HicFindTads(args.matrix, num_processors=args.numberOfProcessors, max_depth=args.maxDepth, File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicexplorer/hicFindTADs.py", line 375, in init self.set_matrix(matrix, pChromosomes) File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicexplorer/hicFindTADs.py", line 396, in set_matrix self.hic_ma = hm.hiCMatrix(pMatrix) File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicmatrix/HiCMatrix.py", line 56, in init matrixFileHandler_load = self.matrixFileHandler.load() File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicmatrix/lib/matrixFileHandler.py", line 51, in load return self.matrixFile.load() File "/home/bz10/usr/miniconda3/lib/python3.8/site-packages/hicmatrix/lib/h5.py", line 35, in load matrix = csr_matrix(tuple([parts['data'], parts['indices'], parts['indptr']]), KeyError: 'data'

Data from GSE77565.

Thanks, Bohan

[joachimwolff]

Hi,

the file ending in command (a) is wrong. First, you write hdf5 instead of h5. However, h5 is our HiCExplorer specific file format, and I don't think a study from 2016 used HiCExplorer to create their files! I know it is a bit confusing, but hdf5 is a generalised container format, we just use it, but the internal structure of the file is specific to HiCExplorer. For (b) you specify a h5 but it tries to load a cool file. And then it complains that certain data structures are not available. This indicates that the file you try to load is neither a HiCExplorer specific h5 nor a cool file.

To confirm my assumption, I downloaded one of the files of the given GSE, and yes, the content looks very different from what we are expecting for HiCExplorer:

Compare to: https://hicexplorer.readthedocs.io/en/latest/content/file-formats.html#interaction-matrix-format-h5

Long story short: Please try to load data formats that HiCExplorer actually supports!

Best,

Joachim

[spiderzbh]

Hi Joachim,

Thank you for the information, that's really helpful. Besides that, I was wondering if it is possible for you to tell me if there is any software I can use to convert the hdf5 files to HiCExplorer specific h5s or cool files.

Thanks, Bohan

[jzohren]

Hi Joachim,

I've run into a similar problem as Bohan. I downloaded publicly available Hi-C data in hdf5 format and would like to convert this to a cool file. I thought that hdf5 and h5 are interchangable file extensions, so I tried with with hicConvertFormat but got essentially the same error as Bohan's Output from B posted above. Any help would be greatly appreciated!

Thanks, Jasmin