Can not proceed without the required Python libraries, please install them and re-run

[Giuseppe1995]

Hi! I am trying to install HiC-Pro 3.1.0 following the instructions on its github page github page. When I try to configure HiC-Pro by typing make configure in HiC-Pro-master directory, but the terminal returns me the following error:

make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt make[1]: Entering directory '/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master' ./scripts/install/install_dependencies.sh -c ./config-install.txt -p /usr/local/bin/ -o /usr/local/bin//HiC-Pro_3.1.0 -q Make sure internet connection works for your shell prompt under current user's privilege ... Starting HiC-Pro installation ! Checking dependencies

• Python libraries ... Can not proceed without the required Python libraries, please install them and re-run make[1]: [scripts/install/Makefile:41: configure] Error 1 make[1]: Leaving directory '/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master' make: [Makefile:40: configure] Error 2

Obviously, I installed all the requested Python libraries trough pip install, as documented here:

pip list

Package Version

bx-python 0.8.11 numpy 1.21.2 pip 21.2.4 pysam 0.17.0 scipy 1.7.1 setuptools 58.0.4 wheel 0.37.0

I can't figure out what I am missing! Giuseppe

[Adeel3Dgenomics]

Hi Giuseppe, Please see the "tmp" folder in ~/HiC-Pro-master , you will find the specific library's error. In my case i was facing 'bx' version conflict and solved using pip install bx-python==0.8.8 try this hope it will help. best, adeel

[Giuseppe1995]

Thank you so much! I have solved this problem as follows: I ran the command cat ${INSTALLATION_DIR}/HiC-Pro-master/check_python.log that gave me the following output:

Traceback (most recent call last): File "/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master/tmp/../scripts/install/check_pythonlib.py", line 69, in import iced ModuleNotFoundError: No module named 'iced'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master/tmp/../scripts/install/check_pythonlib.py", line 73, in raise ImportError('Error - iced cannot be imported') ImportError: Error - iced cannot be imported. So, all I did was to install 'iced' package of Python, and slved the problem. I would therefore suggest to add this package among the dependencies of HiC-Pro-master.

Thank you again, Giuseppe

[chiawenwang]

Thank you so much! I have solved this problem as follows: I ran the command cat ${INSTALLATION_DIR}/HiC-Pro-master/check_python.log that gave me the following output:

Traceback (most recent call last): File "/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master/tmp/../scripts/install/check_pythonlib.py", line 69, in import iced ModuleNotFoundError: No module named 'iced'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master/tmp/../scripts/install/check_pythonlib.py", line 73, in raise ImportError('Error - iced cannot be imported') ImportError: Error - iced cannot be imported. So, all I did was to install 'iced' package of Python, and slved the problem. I would therefore suggest to add this package among the dependencies of HiC-Pro-master.

Thank you again, Giuseppe

hello，I meet the same problem,but I can't find the ${INSTALLATION_DIR}/HiC-Pro-master/check_python.log,there is also no tmp in the HiC-Pro.can u show me your directory file?

[marshals1999]

you'd better download the latest version of Hic-pro software, and tar -zxvf HiC-Pro-3.1.0.tar.gz, and then you will find the config-install.txt file in the stall directory, you need to modify it according to the dependent file install path in your server. such as this:

PREFIX = ### this can be blank or fill your the installation folder path. BOWTIE2_PATH = /anaconda3/bin/bowtie2 SAMTOOLS_PATH = /software/samtools-1.10/samtools R_PATH = /usr/bin/R PYTHON_PATH = /anaconda3/bin/python CLUSTER_SYS = TORQUE

in addition, you need install dependent python modules by "pip install modules name" according to the introduction of HiC-pro software in Github. and finally you can run the command "make configure" and "make install or sudo make install" in the install directory. It will be OK!