search

deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
233 stars 70 forks source link

HiCExplorer crashes on small dataset #666

Closed nservant closed 3 years ago

nservant commented 3 years ago

Hi,

I'm trying to run a few hicExplorer tools on a small Hi-C toy data (SRR4292758 - 500K reads on a yeast genome). It crashes and I'm not sure why actually ... I guess it could be due to the small number of reads, but I would appreciate if you could confirm me.

hicPlotDistVsCounts --matrices SRR4292758_00_20000000_norm.h5  \
                                 --plotFile SRR4292758_00_20000000_norm_distcount.png  \
                                 --outFileData SRR4292758_00_20000000_norm_distcount.txt

Command error:
  Traceback (most recent call last):
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/bin/hicPlotDistVsCounts", line 7, in <module>
      main()
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/hicexplorer/hicPlotDistVsCounts.py", line 321, in main
      mean_dict[matrix_file] = compute_distance_mean(hic_ma, maxdepth=args.maxdepth, perchr=args.perchr)
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/hicexplorer/hicPlotDistVsCounts.py", line 172, in compute_distance_mean
      max_depth_in_bins = int(float(maxdepth * 1.5) / binsize)
  ZeroDivisionError: float division by zero

I also have an error with the TADs calling.

hicFindTADs --matrix SRR4292758_00_40000_norm.h5         
                     --outPrefix tad         
                     --correctForMultipleTesting fdr

Command error:
  INFO:hicexplorer.hicFindTADs:removing diagonal values

  INFO:hicexplorer.hicFindTADs:Computing z-score matrix...

  Traceback (most recent call last):
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/bin/hicFindTADs", line 7, in <module>
      main()
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/hicexplorer/hicFindTADs.py", line 1376, in main
      ft.compute_spectra_matrix()
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/hicexplorer/hicFindTADs.py", line 1068, in compute_spectra_matrix
      self.hic_ma.convert_to_zscore_matrix(maxdepth=self.max_depth * 2.5, perchr=perchr)
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/hicmatrix/HiCMatrix.py", line 352, in convert_to_zscore_matrix
      return self.convert_to_obs_exp_matrix(maxdepth=maxdepth, zscore=True, perchr=perchr)
    File "/home/nservant/Apps/conda/envs/nf-core-hic-dev3/lib/python3.7/site-packages/hicmatrix/HiCMatrix.py", line 477, in convert_to_obs_exp_matrix
      sum_counts = np.bincount(dist_list, weights=submatrix.data)
    File "<__array_function__ internals>", line 6, in bincount
  ValueError: 'list' argument must have no negative elements

Thanks

joachimwolff commented 3 years ago

Does hicInfo -m yourmatrix.h5 work? If yes, can you post the output? And as always: What version of HiCExplorer do you use? Please check if it is the latest 3.6 version; if not, install it and try again. Maybe your bug was already fixed.

nservant commented 3 years ago 
hicInfo -m SRR4292758_00_250000_norm.h5

File:   SRR4292758_00_250000_norm.h5
Size:   238
Bin_length: 0
Sum of matrix:  114.52826509349607
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Non-zero elements:  13,716
Minimum (non zero): 0.00047945626881945537
Maximum:    2.878809938275631
NaN bins:   54
nservant commented 3 years ago

I'm using the version 3.4.3 I cannot install the 3.6, anything special ?

 conda install bioconda::hicexplorer=3.6
PackagesNotFoundError: The following packages are not available from current channels:
joachimwolff commented 3 years ago

Please use conda environments to make sure there is no interference with already installed software:

conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge and activate the environment: conda activate hicexplorer

joachimwolff commented 3 years ago 
Size:   238
Bin_length: 0
Sum of matrix:  114.52826509349607
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Non-zero elements:  13,716
Minimum (non zero): 0.00047945626881945537
Maximum:    2.878809938275631
NaN bins:   54

Sum of matrix is 114, a bin length of 0 and 13,716 non-zero entries?! These are very odd numbers, bin length is usually at least 1000, better 10,000; however, I don't know how frequent the cut sites are in the yeast genome. But these numbers explain to me my why the commands are crashing, you basically apply the algorithms on no data.

nservant commented 3 years ago

I do have 30K contacts in the raw data, but I guess that the balancing removed a lot of data ... I'm creating the h5 data from a balanced cool file, so I guess the h5 file is based on the normalized data ? not the raw counts ?

nservant commented 3 years ago

The same error occurs with hicexplorer 3.6

nservant commented 3 years ago

The same with the raw data (non balanced)

# Matrix information file. Created with HiCExplorer's hicInfo version 3.6
File:   SRR4292758_00_250000_norm.h5
Size:   238
Bin_length: 0
Sum of matrix:  24934.0
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Non-zero elements:  14,377
Minimum (non zero): 1
Maximum:    307
NaN bins:   9
nservant commented 3 years ago

I'm not sure to see how the Bin_length is calculated ? and why it is 0 ?

joachimwolff commented 3 years ago

What is the output of the cool file using hicInfo -m matrix.cool and hicInfo -m matrix.cool --no_metadata?

Hi-C data is always binned, and this is configured at the creation time of the matrix or if you change the resolution.

Considering your chromosomes, the majority is very small, maybe you can remove all of size < 10,000 bp? For example, gi|696449450|gb|JRIU01000025.1|: 697 bp I doubt there is a restriction cut site in this area, maybe at maximum there is one. The information content for Hi-C is more or less not present.

Anyway, why don't you use the cool files directly if you have them for your calculations? HiCExplorer supports the cool format natively.

nservant commented 3 years ago

When I was reading the hicExplorer manual, I undestood that data has to be in h5 format. But indeed, it's easier if I can work with cool file directly !

hicInfo -m SRR4292758_00_250000_norm.cool
# Matrix information file. Created with HiCExplorer's hicInfo version 3.4.3
File:   SRR4292758_00_250000_norm.cool
Date:   2021-02-02T17:25:54.060094
Genome assembly:    unknown
Size:   238
Bin_length: 250000
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Number of chromosomes:  236
Non-zero elements:  7,270
The following columns are available: ['chrom' 'start' 'end' 'weight']

Generated by:   cooler-0.8.6.post0
hicInfo -m SRR4292758_00_250000_norm.cool --no_metadata
# Matrix information file. Created with HiCExplorer's hicInfo version 3.4.3
File:   SRR4292758_00_250000_norm.cool
Size:   238
Bin_length: 0
Sum of matrix:  114.52826509349607
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Non-zero elements:  13,716
Minimum (non zero): 0.00047945626881945537
Maximum:    2.878809938275631
NaN bins:   54
The following columns are available: ['chrom' 'start' 'end' 'weight']
joachimwolff commented 3 years ago

The numbers are different, that should not be. Before I make a closer investigation, please use the latest 3.6 version of HiCExplorer for this command and not the outdated 3.4.

The first output shows a bin size of 250k. Considering the sizes of your chromosomes, it means that more or less all are represented by one (!) pixel, and two with two pixels. If this is just toy data, alright, but don't expect to be able to call TADs. Usually, a few hundred regions per chromosome are expected, not just one. However, the software should not crash and we should improve this. But the output will be just empty.

nservant commented 3 years ago

yes that a very very small set of reads for continuous integration. I may consider increasing the size of input data .... Let me know if you want the cool file(s)

# Matrix information file. Created with HiCExplorer's hicInfo version 3.6
File:   SRR4292758_00_250000_norm.cool
Date:   2021-02-02T17:25:54.060094
Genome assembly:    unknown
Size:   238
Bin_length: 250000
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Number of chromosomes:  236
Non-zero elements:  7,270
The following columns are available: ['chrom' 'start' 'end' 'weight']

Generated by:   cooler-0.8.6.post0
hicInfo -m SRR4292758_00_250000_norm.cool --no_metadata
# Matrix information file. Created with HiCExplorer's hicInfo version 3.6
File:   SRR4292758_00_250000_norm.cool
Size:   238
Bin_length: 0
Sum of matrix:  114.52826509349607
Chromosomes:length: gi|696449538|gb|JRIU01000001.1|: 9053 bp; gi|696449534|gb|JRIU01000002.1|: 114563 bp; gi|696449531|gb|JRIU01000003.1|: 65673 bp; gi|696449527|gb|JRIU01000004.1|: 81668 bp; gi|696449519|gb|JRIU01000006.1|: 81554 bp; gi|696449516|gb|JRIU01000007.1|: 260032 bp; gi|696449512|gb|JRIU01000008.1|: 13055 bp; gi|696449507|gb|JRIU01000009.1|: 57716 bp; gi|696449503|gb|JRIU01000010.1|: 32399 bp; gi|696449498|gb|JRIU01000011.1|: 1490 bp; gi|696449494|gb|JRIU01000012.1|: 150181 bp; gi|696449490|gb|JRIU01000013.1|: 8324 bp; gi|696449486|gb|JRIU01000014.1|: 53418 bp; gi|696449480|gb|JRIU01000016.1|: 90696 bp; gi|696449473|gb|JRIU01000018.1|: 100695 bp; gi|696449470|gb|JRIU01000019.1|: 99425 bp; gi|696449463|gb|JRIU01000021.1|: 43940 bp; gi|696449460|gb|JRIU01000022.1|: 2797 bp; gi|696449456|gb|JRIU01000023.1|: 2917 bp; gi|696449453|gb|JRIU01000024.1|: 7628 bp; gi|696449450|gb|JRIU01000025.1|: 697 bp; gi|696449447|gb|JRIU01000026.1|: 92597 bp; gi|696449444|gb|JRIU01000027.1|: 200129 bp; gi|696449436|gb|JRIU01000029.1|: 2889 bp; gi|696449432|gb|JRIU01000030.1|: 102607 bp; gi|696449428|gb|JRIU01000031.1|: 128238 bp; gi|696449424|gb|JRIU01000032.1|: 112697 bp; gi|696449420|gb|JRIU01000033.1|: 63080 bp; gi|696449415|gb|JRIU01000034.1|: 7726 bp; gi|696449411|gb|JRIU01000035.1|: 35501 bp; gi|696449407|gb|JRIU01000036.1|: 41874 bp; gi|696449403|gb|JRIU01000037.1|: 243759 bp; gi|696449398|gb|JRIU01000038.1|: 19970 bp; gi|696449384|gb|JRIU01000041.1|: 80581 bp; gi|696449380|gb|JRIU01000042.1|: 1420 bp; gi|696449376|gb|JRIU01000043.1|: 209686 bp; gi|696449369|gb|JRIU01000045.1|: 19072 bp; gi|696449364|gb|JRIU01000046.1|: 114207 bp; gi|696449360|gb|JRIU01000047.1|: 47648 bp; gi|696449356|gb|JRIU01000048.1|: 16579 bp; gi|696449352|gb|JRIU01000049.1|: 2689 bp; gi|696449349|gb|JRIU01000050.1|: 8978 bp; gi|696449341|gb|JRIU01000052.1|: 65944 bp; gi|696449337|gb|JRIU01000053.1|: 8106 bp; gi|696449333|gb|JRIU01000054.1|: 4663 bp; gi|696449329|gb|JRIU01000055.1|: 66600 bp; gi|696449325|gb|JRIU01000056.1|: 89927 bp; gi|696449321|gb|JRIU01000057.1|: 49255 bp; gi|696449318|gb|JRIU01000058.1|: 78266 bp; gi|696449312|gb|JRIU01000060.1|: 41077 bp; gi|696449306|gb|JRIU01000062.1|: 228550 bp; gi|696449299|gb|JRIU01000064.1|: 108796 bp; gi|696449294|gb|JRIU01000065.1|: 125219 bp; gi|696449290|gb|JRIU01000066.1|: 4142 bp; gi|696449286|gb|JRIU01000067.1|: 67078 bp; gi|696449279|gb|JRIU01000069.1|: 2222 bp; gi|696449274|gb|JRIU01000070.1|: 71065 bp; gi|696449270|gb|JRIU01000071.1|: 4256 bp; gi|696449267|gb|JRIU01000072.1|: 150714 bp; gi|696449259|gb|JRIU01000074.1|: 85433 bp; gi|696449255|gb|JRIU01000075.1|: 39173 bp; gi|696449251|gb|JRIU01000076.1|: 10056 bp; gi|696449247|gb|JRIU01000077.1|: 20828 bp; gi|696449244|gb|JRIU01000078.1|: 72546 bp; gi|696449240|gb|JRIU01000079.1|: 14050 bp; gi|696449221|gb|JRIU01000084.1|: 25700 bp; gi|696449217|gb|JRIU01000085.1|: 103145 bp; gi|696449212|gb|JRIU01000086.1|: 184319 bp; gi|696449205|gb|JRIU01000088.1|: 190015 bp; gi|696449201|gb|JRIU01000089.1|: 127587 bp; gi|696449190|gb|JRIU01000092.1|: 49227 bp; gi|696449187|gb|JRIU01000093.1|: 29202 bp; gi|696449185|gb|JRIU01000094.1|: 79276 bp; gi|696449182|gb|JRIU01000095.1|: 38291 bp; gi|696449173|gb|JRIU01000097.1|: 46547 bp; gi|696449169|gb|JRIU01000098.1|: 8525 bp; gi|696449165|gb|JRIU01000099.1|: 89607 bp; gi|696449159|gb|JRIU01000100.1|: 54648 bp; gi|696449155|gb|JRIU01000101.1|: 79474 bp; gi|696449148|gb|JRIU01000103.1|: 86887 bp; gi|696449145|gb|JRIU01000104.1|: 42339 bp; gi|696449136|gb|JRIU01000108.1|: 29787 bp; gi|696449131|gb|JRIU01000109.1|: 10760 bp; gi|696449128|gb|JRIU01000110.1|: 6782 bp; gi|696449112|gb|JRIU01000112.1|: 7027 bp; gi|696449104|gb|JRIU01000115.1|: 16715 bp; gi|696449101|gb|JRIU01000116.1|: 59626 bp; gi|696449094|gb|JRIU01000118.1|: 1687 bp; gi|696449086|gb|JRIU01000120.1|: 9674 bp; gi|696449082|gb|JRIU01000121.1|: 59584 bp; gi|696449078|gb|JRIU01000122.1|: 140950 bp; gi|696449074|gb|JRIU01000123.1|: 117283 bp; gi|696449071|gb|JRIU01000124.1|: 23266 bp; gi|696449068|gb|JRIU01000125.1|: 43186 bp; gi|696449064|gb|JRIU01000126.1|: 133998 bp; gi|696449059|gb|JRIU01000127.1|: 24131 bp; gi|696449052|gb|JRIU01000129.1|: 20041 bp; gi|696449046|gb|JRIU01000131.1|: 70561 bp; gi|696449043|gb|JRIU01000132.1|: 36633 bp; gi|696449040|gb|JRIU01000133.1|: 336272 bp; gi|696449035|gb|JRIU01000135.1|: 68146 bp; gi|696449032|gb|JRIU01000136.1|: 10620 bp; gi|696449029|gb|JRIU01000137.1|: 124619 bp; gi|696449025|gb|JRIU01000138.1|: 49460 bp; gi|696449017|gb|JRIU01000140.1|: 34873 bp; gi|696449013|gb|JRIU01000141.1|: 71009 bp; gi|696449009|gb|JRIU01000142.1|: 68880 bp; gi|696449005|gb|JRIU01000143.1|: 1433 bp; gi|696449001|gb|JRIU01000144.1|: 32124 bp; gi|696448998|gb|JRIU01000145.1|: 36783 bp; gi|696448994|gb|JRIU01000146.1|: 16573 bp; gi|696448990|gb|JRIU01000147.1|: 40134 bp; gi|696448986|gb|JRIU01000148.1|: 14492 bp; gi|696448982|gb|JRIU01000149.1|: 23978 bp; gi|696448974|gb|JRIU01000151.1|: 6540 bp; gi|696448971|gb|JRIU01000152.1|: 4818 bp; gi|696448968|gb|JRIU01000153.1|: 4096 bp; gi|696448966|gb|JRIU01000154.1|: 193654 bp; gi|696448963|gb|JRIU01000155.1|: 23523 bp; gi|696448962|gb|JRIU01000156.1|: 11105 bp; gi|696448956|gb|JRIU01000158.1|: 117423 bp; gi|696448953|gb|JRIU01000159.1|: 1845 bp; gi|696448940|gb|JRIU01000163.1|: 103880 bp; gi|696448936|gb|JRIU01000164.1|: 133823 bp; gi|696448927|gb|JRIU01000166.1|: 20288 bp; gi|696448924|gb|JRIU01000167.1|: 37245 bp; gi|696448916|gb|JRIU01000169.1|: 19962 bp; gi|696448912|gb|JRIU01000170.1|: 20198 bp; gi|696448894|gb|JRIU01000175.1|: 3459 bp; gi|696448891|gb|JRIU01000176.1|: 126538 bp; gi|696448887|gb|JRIU01000177.1|: 76725 bp; gi|696448883|gb|JRIU01000178.1|: 15028 bp; gi|696448863|gb|JRIU01000183.1|: 110511 bp; gi|696448860|gb|JRIU01000184.1|: 35488 bp; gi|696448856|gb|JRIU01000185.1|: 11680 bp; gi|696448852|gb|JRIU01000186.1|: 75952 bp; gi|696448848|gb|JRIU01000187.1|: 24915 bp; gi|696448844|gb|JRIU01000188.1|: 93523 bp; gi|696448841|gb|JRIU01000189.1|: 9852 bp; gi|696448836|gb|JRIU01000191.1|: 172874 bp; gi|696448833|gb|JRIU01000192.1|: 114136 bp; gi|696448830|gb|JRIU01000193.1|: 2184 bp; gi|696448827|gb|JRIU01000194.1|: 3526 bp; gi|696448824|gb|JRIU01000195.1|: 17280 bp; gi|696448820|gb|JRIU01000196.1|: 1537 bp; gi|696448808|gb|JRIU01000199.1|: 103298 bp; gi|696448804|gb|JRIU01000200.1|: 18433 bp; gi|696448800|gb|JRIU01000201.1|: 241589 bp; gi|696448796|gb|JRIU01000202.1|: 18939 bp; gi|696448792|gb|JRIU01000203.1|: 30927 bp; gi|696448777|gb|JRIU01000207.1|: 6441 bp; gi|696448773|gb|JRIU01000208.1|: 46428 bp; gi|696448765|gb|JRIU01000210.1|: 26756 bp; gi|696448758|gb|JRIU01000212.1|: 97056 bp; gi|696448754|gb|JRIU01000213.1|: 100299 bp; gi|696448747|gb|JRIU01000215.1|: 40602 bp; gi|696448743|gb|JRIU01000216.1|: 85747 bp; gi|696448739|gb|JRIU01000217.1|: 38622 bp; gi|696448731|gb|JRIU01000219.1|: 68300 bp; gi|696448728|gb|JRIU01000220.1|: 74430 bp; gi|696448724|gb|JRIU01000221.1|: 59649 bp; gi|696448720|gb|JRIU01000222.1|: 66247 bp; gi|696448708|gb|JRIU01000225.1|: 37117 bp; gi|696448701|gb|JRIU01000227.1|: 161315 bp; gi|696448697|gb|JRIU01000228.1|: 58506 bp; gi|696448693|gb|JRIU01000229.1|: 15387 bp; gi|696448690|gb|JRIU01000230.1|: 162216 bp; gi|696448681|gb|JRIU01000233.1|: 5473 bp; gi|696448672|gb|JRIU01000235.1|: 74472 bp; gi|696448666|gb|JRIU01000237.1|: 25567 bp; gi|696448662|gb|JRIU01000238.1|: 3011 bp; gi|696448654|gb|JRIU01000240.1|: 61119 bp; gi|696448646|gb|JRIU01000242.1|: 26286 bp; gi|696448643|gb|JRIU01000243.1|: 9473 bp; gi|696448640|gb|JRIU01000244.1|: 40110 bp; gi|696448634|gb|JRIU01000246.1|: 38089 bp; gi|696448631|gb|JRIU01000247.1|: 126718 bp; gi|696448624|gb|JRIU01000249.1|: 103684 bp; gi|696448621|gb|JRIU01000250.1|: 1881 bp; gi|696448613|gb|JRIU01000252.1|: 102309 bp; gi|696448609|gb|JRIU01000253.1|: 162921 bp; gi|696448601|gb|JRIU01000255.1|: 68639 bp; gi|696448592|gb|JRIU01000257.1|: 3663 bp; gi|696448585|gb|JRIU01000259.1|: 39731 bp; gi|696448564|gb|JRIU01000264.1|: 2795 bp; gi|696448560|gb|JRIU01000265.1|: 16337 bp; gi|696448533|gb|JRIU01000272.1|: 6186 bp; gi|696448510|gb|JRIU01000278.1|: 387 bp; gi|696448473|gb|JRIU01000288.1|: 2257 bp; gi|696448458|gb|JRIU01000292.1|: 2913 bp; gi|696448448|gb|JRIU01000295.1|: 1382 bp; gi|696448423|gb|JRIU01000302.1|: 2264 bp; gi|696448396|gb|JRIU01000309.1|: 4416 bp; gi|696448379|gb|JRIU01000313.1|: 2343 bp; gi|696448356|gb|JRIU01000318.1|: 2936 bp; gi|696448352|gb|JRIU01000319.1|: 15446 bp; gi|696448348|gb|JRIU01000320.1|: 19759 bp; gi|696448335|gb|JRIU01000323.1|: 1059 bp; gi|696448332|gb|JRIU01000324.1|: 4966 bp; gi|696448307|gb|JRIU01000329.1|: 241 bp; gi|696448299|gb|JRIU01000330.1|: 256 bp; gi|696448296|gb|JRIU01000331.1|: 901 bp; gi|696448292|gb|JRIU01000332.1|: 386 bp; gi|696448289|gb|JRIU01000333.1|: 785 bp; gi|696448287|gb|JRIU01000334.1|: 433 bp; gi|696448284|gb|JRIU01000335.1|: 584 bp; gi|696448282|gb|JRIU01000336.1|: 216 bp; gi|696448280|gb|JRIU01000337.1|: 282 bp; gi|696448276|gb|JRIU01000338.1|: 479 bp; gi|696448272|gb|JRIU01000339.1|: 387 bp; gi|696448268|gb|JRIU01000340.1|: 278 bp; gi|696448264|gb|JRIU01000341.1|: 236 bp; gi|696448260|gb|JRIU01000342.1|: 303 bp; gi|696448257|gb|JRIU01000343.1|: 220 bp; gi|696448253|gb|JRIU01000344.1|: 210 bp; gi|696448250|gb|JRIU01000345.1|: 344 bp; gi|696448247|gb|JRIU01000346.1|: 394 bp; gi|696448244|gb|JRIU01000347.1|: 210 bp; gi|696448241|gb|JRIU01000348.1|: 216 bp; gi|696448237|gb|JRIU01000349.1|: 309 bp; gi|696448233|gb|JRIU01000350.1|: 730 bp; gi|696448229|gb|JRIU01000351.1|: 781 bp; gi|696448226|gb|JRIU01000352.1|: 244 bp; gi|696448223|gb|JRIU01000353.1|: 222 bp; gi|696448219|gb|JRIU01000354.1|: 330 bp; gi|696448215|gb|JRIU01000355.1|: 367 bp; gi|696448211|gb|JRIU01000356.1|: 344 bp; gi|696448207|gb|JRIU01000357.1|: 607 bp; gi|696448202|gb|JRIU01000358.1|: 473 bp; gi|696448196|gb|JRIU01000359.1|: 1539 bp; gi|696448178|gb|JRIU01000363.1|: 639 bp; gi|696448170|gb|JRIU01000365.1|: 1642 bp; gi|696448067|gb|JRIU01000392.1|: 2426 bp; gi|696448040|gb|JRIU01000400.1|: 6091 bp; gi|696448022|gb|JRIU01000406.1|: 4960 bp; gi|696447993|gb|JRIU01000414.1|: 2135 bp; 
Non-zero elements:  13,716
Minimum (non zero): 0.00047945626881945537
Maximum:    2.878809938275631
NaN bins:   54
The following columns are available: ['chrom' 'start' 'end' 'weight']
nservant commented 3 years ago

I will re-run a test with much smaller bin size

nservant commented 3 years ago

It works fine with a 1kb resolution ! So that's ok for me. Thank you for your help

joachimwolff commented 3 years ago

Glad to hear!