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.
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