Hi,
I tried to install the HiNT package using conda. But I got the following error message:

aaa@aaa:~$ conda install hint
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__glibc==2.31=0

Your installed version is: 2.31

I would be very happy if you could tell me how I can solve this problem.
Best,
Daisuke

Hello,

Thank you so much for all of your hard work developing this wonderful tool! I have run HiNT successfully on the test data provided (hg19), but encountered the following error when trying to run it on my own data (hg38).

The command

hint cnv -m /data/test.hic \
   -f juicer \
   --refdir /data/HiNT_ref/refData/hg38 \
   -r 50 \
   -g hg38 \
   -n TEST \
   --bicseq /usr/local/apps/bicseq2/0.7.3/ \
   -e HindIII \
   -o /data/TEST_CNV

The error

From log.out:

[12:57:50] Argument List: 
[12:57:50] Hi-C contact matrix = /data/test.hic
[12:57:50] Hi-C contact matrix format = juicer
[12:57:50] resolution = 50 kb
[12:57:50] Genome = hg38
[12:57:50] BICseq directory = /usr/local/apps/bicseq2/0.7.3/
[12:57:50] Name = TEST
[12:57:50] Output directory = /data/TEST_CNV
HiC version:  8
One of the chromosomes wasn't found in the file. Check that the chromosome name matches the genome.

From log.err:

Traceback (most recent call last):
  File "/usr/local/apps/hint/2.2.7/bin/hint", line 201, in <module>
    main()
  File "/usr/local/apps/hint/2.2.7/bin/hint", line 194, in main
    cnvrun(argparser)
  File "/usr/local/Anaconda/envs_app/hint/2.2.7/lib/python3.6/site-packages/HiNT/runhint.py", line 79, in cnvrun
    rowSumFilesInfo = getGenomeRowSums(opts.resolution, opts.matrixfile, chromlf, opts.outdir,opts.name)
  File "/usr/local/Anaconda/envs_app/hint/2.2.7/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 69, in getGenomeRowSums
    sumInfo = getSumPerChrom(i, j, hicfile, binsize, chroms, chromInfo, sumInfo)
  File "/usr/local/Anaconda/envs_app/hint/2.2.7/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 20, in getSumPerChrom
    result = straw('NONE', hicfile, str(chr1), str(chr2), 'BP', binsize)
  File "/usr/local/Anaconda/envs_app/hint/2.2.7/lib/python3.6/site-packages/HiNT/straw.py", line 471, in straw
    master=list1[0]
TypeError: 'int' object is not subscriptable

Potential issue

It seems that the issue is happening due to lines 18-19 in the getGenomeRowSumsFromHiC.py script. These lines trim the "chr" string from the chromosome names before passing them to the straw function.

However, for hg38 (at least for the .hic file I am working with), straw will only work when the "chr" string is included. For example, straw("NONE", "/data/test.hic", "chr1", "chr1", "BP", 50000) works and returns data, while straw("NONE", "/data/test.hic", "1", "1", "BP", 50000) does not work and returns the same error as seen when launching HiNT CNV.

Possible solution?

One solution would be to remove these lstrip functions from the script. However, this might cause issues for other genome builds (i.e. hg19). If these chromosome names are being taken from the hg19.len and hg38.len files, then this solution could still work with hg19 by just removing the "chr" strings there, although I am not sure if that would affect other steps.

I completely understand if that is too disruptive of a change to make. I wanted to still post this regardless in case any other users are experiencing similar difficulties.

Hi, I tried to run hint cnv and got these error messages.

open: No such file or directory
Traceback (most recent call last):
File "/data2/home/song7602/Tools/HiNT/bin/hint", line 202, in
main()
File "/data2/home/song7602/Tools/HiNT/bin/hint", line 194, in main
cnvrun(argparser)
File "/data2/home/song7602/Tools/HiNT/HiNT/runhint.py", line 86, in cnvrun
chroms,regressionFileAllchroms,regressionChromFilesInfo = prepareData(opts.name,opts.outdir,opts.referencedir,chromlf,rowSumFilesInfo,binsize,GCPercent_1kb,mappablity_track,restrictionSites) #Prepare the other data Information for regression
File "/data2/home/song7602/Tools/HiNT/HiNT/prepare_regression.py", line 167, in prepareData
mapscore = getmappability(mappablity_track, chrom, 1, chromLength, resolution)
File "/data2/home/song7602/Tools/HiNT/HiNT/prepare_regression.py", line 42, in getmappability
tb = tabix.open(mappablity_track)
tabix.TabixError: Can't open the index file.

is mappability_track file required as an input for running hint cnv? and if it is, which path should it be located in? at reference genome directory?

Hi, any chance you could reset the links of the supplementary files so that they can be access?

Thanks.

Hi, Dear HiNT developer,
Thanks for developing this HiNT. I have successfully installed HiNT. I am using hint tl. But it always return ERROR: path to the matrixfile is not valid. I am very sure that the full file path for matrixfile(.hic) /home/XX/testData/test.hic is there. Could you tell me the path is absolute path or relative path? Could you give me a real example how to use this commandline, how to configure the file path? I tried absolute path and relative path, but it always return ERROR: path to the matrixfile is not valid.
Thank you in advance!
My command line is as the following
hint tl -m /home/WZ/testData/test.hic -f juicer --refdir /home/WZ/HiNT_Reference/hg19 --backdir /home/WZ/HiNT_Background/hg19 -g hg19 -n test -c 0.05 --ppath /home/WZ/pairix -p 8 -o test

HiNT is really powerful. Can you show how to make reference files for other species, which will extend its applications.

When trying to run the program with mm10, I get the error {pandas.errors.EmptyDataError: No columns to parse from file} because the mm10_1kb_GCPercent.bed downloaded from the references is empty. Can the actual reference file be uploaded please?

when i try to test the code by testdata,，it has some question like"MemoryError: Unable to allocate 18.7 GiB for an array with shape (50095, 50095) and data type float64".how can i resolve this problem

Hi, I tried to use your docker on coolers files:

$ hint tl -m out/wtg2nolabelfc1_1000kb.cool,out/wtg2nolabelfc1_100kb.cool --chimeric out/wtg2nolabelfc1_chimeric.sorted.pairsam.gz --refdir data/hg19_SNPs --backdir backgroundMatrices/hg19 --ppath /miniconda3/bin/pairix -f cooler -g hg19 -n test -o out_tl_new

[15:48:22] Argument List: 
[15:48:22] Hi-C contact matrix = out/wtg2nolabelfc1_1000kb.cool, out/wtg2nolabelfc1_100kb.cool
[15:48:22] Hi-C contact matrix format = cooler
[15:48:22] Hi-C chimeric read pairs = out/wtg2nolabelfc1_chimeric.sorted.pairsam.gz
[15:48:22] Genome = hg19
[15:48:22] Name = test
[15:48:22] Output directory = out_tl_new
[15:48:22] Prepare Matrices!
Traceback (most recent call last):
  File "/miniconda3/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2657, in get_loc
    return self._engine.get_loc(key)
  File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 129, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index_class_helper.pxi", line 91, in pandas._libs.index.Int64Engine._check_type
KeyError: 'chrom'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/miniconda3/bin/hint", line 201, in <module>
    main()
  File "/miniconda3/bin/hint", line 197, in main
    translrun(argparser)
  File "/miniconda3/lib/python3.6/site-packages/HiNT/runhint.py", line 108, in translrun
    matrix1MbInfo = coolToMatrix(matrixfile1Mb,1000,opts.outdir,opts.name)
  File "/miniconda3/lib/python3.6/site-packages/HiNT/coolToMatrix.py", line 30, in coolToMatrix
    binsInfo = getBins(coolfile)
  File "/miniconda3/lib/python3.6/site-packages/HiNT/coolToMatrix.py", line 9, in getBins
    idxarray = np.where(coolfile.bins()["chrom"][:] == chrom)
  File "/miniconda3/lib/python3.6/site-packages/cooler/core.py", line 532, in __getitem__
    return self._slice(self.fields, lo, hi)
  File "/miniconda3/lib/python3.6/site-packages/cooler/api.py", line 246, in _slice
    return bins(grp, lo, hi, fields, **kwargs)
  File "/miniconda3/lib/python3.6/site-packages/cooler/api.py", line 448, in bins
    is_integer_dtype(out['chrom'].dtype)
  File "/miniconda3/lib/python3.6/site-packages/pandas/core/series.py", line 868, in __getitem__
    result = self.index.get_value(self, key)
  File "/miniconda3/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 4360, in get_value
    iloc = self.get_loc(key)
  File "/miniconda3/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2659, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 129, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index_class_helper.pxi", line 91, in pandas._libs.index.Int64Engine._check_type
KeyError: 'chrom' 

This happens with existing coolers and with coolers generated by your 'hint pre' pipeline.

Hi, thank you for your good software.
I am studying plant 3D genome. For both HiNT-CNV and HiNT-TL, the parameter --refdir directs to specific human genomes. Does that mean this software can only be applied to hic matrix from human genomes? Can you provide some modifications for other reference genomes?
Hope to hear from you. Thank you so much!

Pengcheng

hello,
I want to run hint tl for other species , Is background matrices necessary ?

I am curious that I can get background matrix for the reference, mRatNor1, https://vgp.github.io/genomeark/Rattus_norvegicus/

Can I make background matrix myself?

for example, if we use -n HiC_K562 as prefix name. The string parsers may get wrong results. like

chrompair = paste(strsplit(matrix,'_')[[1]][2],strsplit(matrix,'_')[[1]][3],sep="_")

in externalScripts/getBreakPoints2steps.R

Hello,

Thanks for developing hint, the paper is super interesting! I tried to identify translocations for 12 samples, 6 completed successfully and for 6 of them I am getting the following one of these error messages:

IndexError: list index out of range
IndexError: index 1125 is out of bounds for axis 0 with size 592

I'm also attaching the complete log files that end up in these errors.

Would you have any advice on how to fix this?
Thanks!
Alejandro

Job_806491.txt
Job_806495.txt

Hi, I'm trying to run hint cnv but keep getting this error. When I run hint after installation, i don't get any error that it installed wrong.

-bash:login01:/broad/hptmp/mtegtmey/HiNT/bin 1101 $ python hint cnv -m /broad/hptmp/mtegtmey/work/NFID_0514/NFID0514_D28.hic -f juicer --refdir /broad/hptmp/mtegtmey/HiNT/references/hg19 -r 50 -g hg19 -n d28_del -o /broad/hptmp/mtegtmey/work/NFID_0514/d28_cnv --bicseq /broad/hptmp/mtegtmey/BICseq2-seg_v0.7.3/ -e MboI
Traceback (most recent call last):
File "hint", line 201, in
main()
File "hint", line 193, in main
from HiNT.runhint import cnvrun
ModuleNotFoundError: No module named 'HiNT'
-bash:login01:/broad/hptmp/mtegtmey/HiNT/bin 1102 $

Hi,
I got the following error when using the test data:
$ hint pre -d /fdb/hint/testData/TestSub_1.fq.gz,/fdb/hint/testData/TestSub_2.fq.gz
-i /fdb/hint/bwaIndex/hg19/hg19.fa
--refdir /fdb/hint/references/hg19
--informat fastq
--outformat juicer
-g hg19
-n test1
-o /data/apptest2/test1out
--samtoolspath /usr/local/apps/samtools/1.9/bin/samtools
-p 4
--pairtoolspath /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools
-a /usr/local/Anaconda/envs_app/hint/2.2.7/bin/bwa
…
...
/usr/local/apps/samtools/1.9/bin/samtools view -h /data/apptest2/test1out/test1.bam | /usr/local/Anaconda/envs_app/hint/2.2.7/
bin/pairtools parse -c /fdb/hint/references/hg19/hg19.len -o /data/apptest2/test1out/test1.pairsam.gz --nproc-in 4 --nproc-out
4 --assembly hg19
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools sort -o /data/apptest2/test1out/test1.sorted.pairsam.gz --memory 20G --c
ompress-program gzip --nproc-in 4 --nproc-out 4 --tmpdir /data/apptest2/test1out/tmp /data/apptest2/test1out/test1.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools select --nproc-in 4 --nproc-out 4 --chrom-subset /fdb/hint/references/hg
19/hg19.len -o /data/apptest2/test1out/test1_valid.sorted.pairsam.gz '(pair_type == "UU") or (pair_type == "UR") or (pair_type
== "RU")' /data/apptest2/test1out/test1.sorted.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools select --nproc-in 4 --nproc-out 4 -o /data/apptest2/test1out/test1_chime
ric.sorted.pairsam.gz '(pair_type == "NR") or (pair_type == "CC") or (pair_type == "MR")' /data/apptest2/test1out/test1.sorted
.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools dedup --nproc-in 4 --nproc-out 4 --output /data/apptest2/test1out/test1_valid.sorted.deduped.pairsam.gz /data/apptest2/test1out/test1_valid.sorted.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools split --nproc-in 4 --nproc-out 4 --output-pairs /data/apptest2/test1out/test1_merged_valid.pairs.gz /data/apptest2/test1out/test1_valid.sorted.deduped.pairsam.gz
pairix -f /data/apptest2/test1out/test1_merged_valid.pairs.gz
java -jar None pre -n /data/apptest2/test1out/test1_merged_valid.pairs.gz /data/apptest2/test1out/test1.hic hg19
Error: Unable to access jarfile None
java -jar None addNorm -d -w 5000 -F /data/apptest2/test1out/test1.hic
Error: Unable to access jarfile None

$ which java
/usr/local/Java/jdk1.8.0_11/bin/java

I would really appreciate if someone can help with this.

Regards,

Jean

Hi Park lab,

I'll start by saying thanks for all the work put into this package and having it support a bunch of input file formats.
That's really great and makes it easy for people to use this tool.

The issue

When running the cnv subcommand, the CNV callings starts off normally, but it fails when running the first set of rowsums.
Here is an example output (cooler input file, hg38 genome).

...
chr1 chrX
Writing rowsums of chr1!
Traceback (most recent call last):
  File "/mnt/work1/users/home2/hawleyj/miniconda3/envs/hint/bin/hint", line 203, in <module>
    main()
  File "/mnt/work1/users/home2/hawleyj/miniconda3/envs/hint/bin/hint", line 196, in main
    cnvrun(argparser)
  File "/mnt/work1/users/home2/hawleyj/miniconda3/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromCool.py", line 31, in getSumPerChrom
    writeGenomeRowSums(coolfile,chromRowsums,chrom1,outputname,name)
  File "/mnt/work1/users/home2/hawleyj/miniconda3/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromCool.py", line36, in writeGenomeRowSums
    allbins = bins[bins['chrom']== chrom].ix[:0:3]
  File "/mnt/work1/users/home2/hawleyj/miniconda3/envs/hint/lib/python3.6/site-packages/pandas/core/generic.py", line 5141, in __getattr__
    reutnr object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

Potential problem source

The most likely culprit is the .ix pandas DataFrame method in this line
This is because the .ix method became deprecated in v0.20.0 of Pandas, and was finally removed in the v1.0 release.

Possible solutions

Currently, in setup.py and requirements.txt, the Pandas version is specified as pandas>=0.23.0.
This could be capped below v1.0.0 with pandas>=0.23.0,<1.0.0.

Or, to extend the longevity of the tool, the .ix method could be swapped out in favour of .iloc or a related method.

I don't know how extensive the issue may be, but searching the repository only returns the single instance in getGenomeRowSumsFromCool.py, so this may be a simple fix.

Installation configuration details, if helpful

Hi,

I'm experiencing the following error when I'm running hint cnv using a juicer .hic file as input, both with my own and the test dataset.

$ hint cnv -f juicer -m test.hic --refdir hg19 --bicseq /home/projects/cu_10027/apps/software/BICseq2-seg_v0.7.3 -e MboI -r 50000 -g hg19 -o ./ -n test -p 12
[15:32:05] Argument List:
[15:32:05] Hi-C contact matrix = test.hic
[15:32:05] Hi-C contact matrix format = juicer
[15:32:05] resolution = 50000 kb
[15:32:05] Genome = hg19
[15:32:05] BICseq directory = /home/projects/cu_10027/apps/software/BICseq2-seg_v0.7.3
[15:32:05] Name = test
[15:32:05] Output directory = ./
HiC version:  8
Error finding block data

Traceback (most recent call last):
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/bin/hint", line 201, in <module>
    main()
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/bin/hint", line 194, in main
    cnvrun(argparser)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/runhint.py", line 79, in cnvrun
    rowSumFilesInfo = getGenomeRowSums(opts.resolution, opts.matrixfile, chromlf, opts.outdir,opts.name)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 69, in getGenomeRowSums
    sumInfo = getSumPerChrom(i, j, hicfile, binsize, chroms, chromInfo, sumInfo)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/getGenomeRowSumsFromHiC.py", line 20, in getSumPerChrom
    result = straw('NONE', hicfile, str(chr1), str(chr2), 'BP', binsize)
  File "/home/projects/cu_10027/apps/software/miniconda3/4.5.4/envs/hint/lib/python3.6/site-packages/HiNT/straw.py", line 543, in straw
    blockBinCount=list1[0]
TypeError: 'int' object is not subscriptable

I installed Hint using miniconda3/4.5.4 and python=3.6
Is there any known workaround?

Thanks,
Nikos

I downloaded the fastq files, reference files and background matrix for hg19 in test directory.
then I ran successfully the "pre" step.
When I ran the tl command, I got the following error message:
hint tl -m ./HiNT_test_cooler/test_1000kb.cool,./HiNT_test_cooler/test_100kb.cool --chimeric ./HiNT_test_cooler/test_chimeric.sorted.pairsam.gz --refdir ./HiNT/references/hg19 --backdir ./HiNT/backgroundM/hg19 --ppath ./anaconda3/envs/pybio/bin/pairix -f cooler -g hg19 -n test -o HiNT_test_tl

OSError: HiNT_test_tl/InterMap_matrix/test_1000kb_chr8_chr16_InterMap_matrix.txt not found.

I got the same message for my own data even though the chromosome number is different.

Here is my conda list:

Name Version Build Channel

_libgcc_mutex 0.1 main
_r-mutex 1.0.0 anacondar_1
argparse 1.4.0 py35_0 bioconda
asciitree 0.3.3 py_2
binutils_impl_linux-64 2.33.1 he6710b0_7
binutils_linux-64 2.33.1 h9595d00_15
biopython 1.72 py35h04863e7_0
blas 1.1 openblas conda-forge
bokeh 0.13.0 py35_0
bwa 0.7.17 hed695b0_7 bioconda
bwidget 1.9.11 1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2020.1.1 0
cairo 1.14.12 h8948797_3
certifi 2018.8.24 py35_1
click 7.0 py_0
cloudpickle 1.2.2 py_0
cooler 0.8.6 py_0 bioconda
coreutils 8.31 h516909a_0 conda-forge
curl 7.61.0 h84994c4_0
cytoolz 0.9.0.1 py35h14c3975_1
dask 0.19.2 py35_0
dask-core 0.19.2 py35_0
dill 0.2.8.2 py35_0
distributed 1.23.2 py35_0
fontconfig 2.13.0 h9420a91_0
freetype 2.9.1 h8a8886c_1
fribidi 1.0.5 h7b6447c_0
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_15
gfortran_impl_linux-64 7.3.0 hdf63c60_1
gfortran_linux-64 7.3.0 h553295d_15
glib 2.63.1 h5a9c865_0
graphite2 1.3.13 h23475e2_0
gsl 2.4 blas_openblash47a8a8e_1 [blas_openblas] conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_15
h5py 2.8.0 py35h989c5e5_3
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.2 hba1933b_1
heapdict 1.0.1 py_0
hint 2.0.1 py_0 bioconda
htslib 1.9 h4da6232_3 bioconda
icu 58.2 h9c2bf20_1
intel-openmp 2019.4 243
jinja2 2.10.3 py_0
jpeg 9b h024ee3a_2
krb5 1.16.1 hc83ff2d_6
ld_impl_linux-64 2.33.1 h53a641e_7
libcurl 7.61.0 h1ad7b7a_0
libdeflate 1.5 h516909a_0 conda-forge
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 9.1.0 hdf63c60_0
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0
libpng 1.6.37 hbc83047_0
libssh2 1.8.0 h9cfc8f7_4
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_0
libuuid 1.0.3 h1bed415_2
libxcb 1.13 h1bed415_1
libxml2 2.9.9 hea5a465_1
locket 0.2.0 py35h170bc82_1
lz4-c 1.8.1.2 h14c3975_0
make 4.2.1 h1bed415_1
markupsafe 1.0 py35h14c3975_1
mkl 2019.4 243
msgpack-python 0.5.6 py35h6bb024c_1
multiprocess 0.70.5 py35_0 conda-forge
ncurses 6.1 he6710b0_1
numpy 1.14.6 py35_blas_openblashd3ea46f_200 [blas_openblas] conda-forge
openblas 0.2.20 8 conda-forge
openjdk 8.0.152 h46b5887_1
openssl 1.0.2u h7b6447c_0
packaging 20.1 py_0
pairix 0.3.0 py35_0 bioconda
pairtools 0.2.2 py35he8651fa_0 bioconda
pandas 0.23.4 py35h04863e7_0
pango 1.42.4 h049681c_0
partd 1.1.0 py_0
pbgzip 2016.08.04 h2f06484_1 bioconda
pcre 8.43 he6710b0_0
perl 5.26.2 h14c3975_0
pip 10.0.1 py35_0
pixman 0.38.0 h7b6447c_0
psutil 5.4.7 py35h14c3975_0
pyfaidx 0.5.8 py_1 bioconda
pyparsing 2.4.6 py_0
pysam 0.8.4 py35_0 bioconda
python 3.5.6 hc3d631a_0
python-dateutil 2.8.1 py_0
pytz 2019.3 py_0
pyyaml 3.13 py35h14c3975_0
r 3.5.0 r350_0
r-base 3.5.0 h1e0a451_1
r-boot 1.3_20 r350h912f1d8_0
r-cairo 1.5_9 r350hb353451_1
r-class 7.3_14 r350hb353451_4
r-cluster 2.0.7_1 r350h6ecb4d7_0
r-codetools 0.2_15 r350h912f1d8_0
r-foreign 0.8_70 r350hb353451_0
r-kernsmooth 2.23_15 r350h6ecb4d7_4
r-lattice 0.20_35 r350hb353451_0
r-mass 7.3_49 r350hb353451_0
r-matrix 1.2_14 r350hb353451_0
r-mgcv 1.8_23 r350hb353451_0
r-nlme 3.1_137 r350h6ecb4d7_0
r-nnet 7.3_12 r350hb353451_0
r-recommended 3.5.0 r350_0
r-rpart 4.1_13 r350hb353451_0
r-sandwich 2.4_0 r350h912f1d8_0
r-spatial 7.3_11 r350hb353451_4
r-strucchange 1.5_1 r350h912f1d8_0
r-survival 2.42_3 r350hb353451_0
r-zoo 1.8_1 r350hb353451_0
readline 7.0 h7b6447c_5
requests 2.12.5 py35_0 conda-forge
samtools 1.3.1 5 bioconda
scikit-learn 0.19.2 py35_blas_openblasha84fab4_201 [blas_openblas] conda-forge
scipy 1.1.0 py35_blas_openblash7943236_201 [blas_openblas] conda-forge
setuptools 40.2.0 py35_0
six 1.11.0 py35_1 conda-forge
sortedcontainers 2.0.5 py35_0
sqlite 3.30.1 h7b6447c_0
tabix 0.2.6 ha92aebf_0 bioconda
tblib 1.6.0 py_0
tk 8.6.8 hbc83047_0
tktable 2.10 h14c3975_0
toolz 0.10.0 py_0
tornado 5.1.1 py35h7b6447c_0
wheel 0.31.1 py35_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zict 1.0.0 py_0
zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0

Hi, I want to use Hint TL now, but one problem is the enzymes I can choose in the software are DpnII,MboI,HindIII. We use arima in our experiment, so what should I do if the enzyme is not in the software select list？
Thank you!

Hi all,

I am trying to run HiNT on the example dataset, but it keeps failing. I installed hint from Conda, using the following steps:

• conda create -p $(pwd)/hint-env
• conda activate ./hint-env
• conda install -c su hint

It installs without error, and when I run hint --version, I get back hint 2.2.8. I am running on a RHEL8 cluster.

However, I am trying to run this script:

#!/bin/bash
#

hint tl \
  -m ${HINT_DIR}/db/testData/test.hic \
  -f juicer --refdir ${HINT_DIR}/db/refData/hg38/ \
  --backdir ${HINT_DIR}/db/backgroundMatrices/hg38 \
  -g hg38 \
  -n 4DNFICSTCJQZ \
  -c 0.05 \
  --ppath pairix \
  -o HiNTtransl_juicerOUTPUTXX

Whenever I run it, I am faced with the following error:

noderome106 >> ~ # bash run_hint.sh
[09:43:31] Argument List:
[09:43:31] Hi-C contact matrix = ${HINT_ENV}/db/testData/test.hic
[09:43:31] Hi-C contact matrix format = juicer
[09:43:31] Genome = hg38
[09:43:31] Name = 4DNFICSTCJQZ
[09:43:31] Output directory = HiNTtransl_juicerOUTPUTXX
[09:43:31] Prepare Matrices!
HiC version:  8
Traceback (most recent call last):
  File "${HINT_ENV}/bin/hint", line 203, in <module>
    main()
  File "${HINT_ENV}/bin/hint", line 199, in main
    translrun(argparser)
  File "${HINT_ENV}/lib/python3.6/site-packages/HiNT/runhint.py", line 112, in translrun
    matrix1MbInfo = hicToMatrix(opts.matrixfile, 1000, chromlengthf, opts.outdir, opts.name)
  File "${HINT_ENV}/lib/python3.6/site-packages/HiNT/hicToMatrix.py", line 44, in hicToMatrix
    dumpMatrix(chrom1, chrom2, resolution, hicfile, chromInfo,outputname)
  File "${HINT_ENV}/lib/python3.6/site-packages/HiNT/hicToMatrix.py", line 29, in dumpMatrix
    res = coo_matrix((data, (row, col)), shape=(binnumber1, binnumber2)).toarray()
  File "${HINT_ENV}/lib/python3.6/site-packages/scipy/sparse/coo.py", line 196, in __init__
    self._check()
  File "${HINT_ENV}/lib/python3.6/site-packages/scipy/sparse/coo.py", line 283, in _check
    raise ValueError('row index exceeds matrix dimensions')
ValueError: row index exceeds matrix dimensions

This feels like a bug in the software, as I have installed it multiple times, in many different ways, and cannot get past this. I also saw that I user reported this issue a while back, but did not get a response.

FYI: I did not use the env var ${HINT_ENV}. I used full, absolute paths while running the example. I replaced the absolute paths in this comment for security purposes.

Any and all help would be appreciated. Thanks! :)