HiC-Pro error message during installation
Yung-Chih Lai
gary > pwd
/Users/gary/Applications/HiC-Pro-master
gary > ll
total 128
-rwxr-xr-x@ 1 gary staff 2.6K Mar 2 01:16 INSTALL
-rwxr-xr-x@ 1 gary staff 5.8K Mar 2 01:16 LICENSE
-rwxr-xr-x@ 1 gary staff 7.0K Mar 2 01:16 LOGBOOK
-rwxr-xr-x@ 1 gary staff 2.0K Mar 2 01:16 Makefile
-rwxr-xr-x@ 1 gary staff 12K Mar 2 01:16 NEWS
-rwxr-xr-x@ 1 gary staff 12K Mar 2 01:16 README.rst
drwxr-xr-x@ 10 gary staff 340B Mar 2 01:16 annotation/
drwxr-xr-x@ 4 gary staff 136B Mar 2 01:16 bin/
-rwxr-xr-x@ 1 gary staff 2.7K Mar 2 01:16 config-hicpro.txt
-rwxr-xr-x@ 1 gary staff 279B Mar 2 01:16 config-install.txt
-rw-r--r-- 1 gary staff 856B Mar 8 13:45 config-system.txt
drwxr-xr-x@ 19 gary staff 646B Mar 2 01:16 doc/
drwxr-xr-x@ 31 gary staff 1.0K Mar 2 01:16 scripts/
gary > sudo make configure
Password:
make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt
./scripts/install/install_dependencies.sh -c ./config-install.txt -o /HiC-Pro_2.8.1_devel
Make sure internet connection works for your shell prompt under current user's privilege ...
Starting HiC-Pro installation ...
Where should missing software prerequisites be installed ? [/usr/bin]
/Users/gary/Applications
Checking dependencies ...
Checking Python libraries ...
The required Python libraries appear to be already installed.
Checking R installation ...
The required R packages appear to be already installed.
Bowtie2 Aligner appears to be already installed.
Samtools appears to be already installed.
Dependencies checked !
Check HiC-Pro configuration ...
Warning : Scheduler system not defined - Default is Torque/PBS
Configuration for TORQUE/PBS system.
Exit - Cannot install HiCPro in /local/bin directory. Maybe missing super-user (root) permissions to write there. Please specify another directory in the config-install.txt file (PREFIX=)
make[1]: *** [configure] Error 1
make: *** [configure] Error 2
gary >
nservant
Are you sure that you can write in /local/bin/ ?
I would advice to set the prefix to another path, for instance
/Users/gary/Applications/
How do you fill the config-install.txt file ?Thank you
Yung-Chih Lai
/Users/gary/anaconda/bin/python: can't open file 'setup.py': [Errno 2] No such file or directory
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nservant
by
Because, otherwise, you ask HiC-pro to be installed in its current path. Not sure if it will fix the issue, but It should be better ...
Now in theory it will try to install HiCPro in /Users/gary/Applications/HiC-Pro_2.8.1_devel/
Let me know if it is better.
N
On Thursday, 9 March 2017 08:12:10 UTC+1, Yung-Chih Lai wrote:
Hi,
Yung-Chih Lai
gary > pwd
/Users/gary/Applications/HiC-Pro-master
gary > ll
total 120
-rwxr-xr-x@ 1 gary staff 2.6K Mar 2 01:16 INSTALL
-rwxr-xr-x@ 1 gary staff 5.8K Mar 2 01:16 LICENSE
-rwxr-xr-x@ 1 gary staff 7.0K Mar 2 01:16 LOGBOOK
-rwxr-xr-x@ 1 gary staff 2.0K Mar 2 01:16 Makefile
-rwxr-xr-x@ 1 gary staff 12K Mar 2 01:16 NEWS
-rwxr-xr-x@ 1 gary staff 12K Mar 2 01:16 README.rst
drwxr-xr-x@ 10 gary staff 340B Mar 2 01:16 annotation/
drwxr-xr-x@ 4 gary staff 136B Mar 2 01:16 bin/
-rwxr-xr-x@ 1 gary staff 2.7K Mar 2 01:16 config-hicpro.txt
-rwxr-xr-x@ 1 gary staff 304B Mar 10 14:55 config-install.txt
drwxr-xr-x@ 19 gary staff 646B Mar 2 01:16 doc/
drwxr-xr-x@ 31 gary staff 1.0K Mar 2 01:16 scripts/
gary > make configure
make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt
./scripts/install/install_dependencies.sh -c ./config-install.txt -o /Users/gary/Applications/HiC-Pro_2.8.1_devel
Make sure internet connection works for your shell prompt under current user's privilege ...
Starting HiC-Pro installation ...
Where should missing software prerequisites be installed ? [/Users/gary/bin]
/Users/gary/Applications/
Checking dependencies ...
Checking Python libraries ...
The required Python libraries appear to be already installed.
Checking R installation ...
The required R packages appear to be already installed.
Bowtie2 Aligner appears to be already installed.
Samtools appears to be already installed.
Dependencies checked !
Check HiC-Pro configuration ...
Warning : Scheduler system not defined - Default is Torque/PBS
Configuration for TORQUE/PBS system.
gary > make install
(g++ -Wall -O2 -std=c++0x -o build_matrix /Users/gary/Applications/HiC-Pro-master/scripts/src/build_matrix.cpp; mv build_matrix /Users/gary/Applications/HiC-Pro-master/scripts)
/Users/gary/Applications/HiC-Pro-master/scripts/src/build_matrix.cpp:249:7: warning:
private field 'idx' is not used [-Wunused-private-field]
int idx; // really needed ?
^
1 warning generated.
(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /Users/gary/Applications/HiC-Pro-master/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /Users/gary/Applications/HiC-Pro-master/scripts)
(cp /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice /Users/gary/Applications/HiC-Pro-master/scripts; cd /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/; /Users/gary/anaconda/bin/python setup.py install --user;)
cp: /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice: Not a directory
/bin/sh: line 0: cd: /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/: Not a directory
/Users/gary/anaconda/bin/python: can't open file 'setup.py': [Errno 2] No such file or directory
make: *** [iced] Error 2
gary > cat config-install.txt
#########################################################################
## Paths and Settings - Start editing here !
#########################################################################
PREFIX = /Users/gary/Applications/
BOWTIE2_PATH =
SAMTOOLS_PATH =
R_PATH =
PYTHON_PATH =
CLUSTER_SYS =
gary >
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nservant
(cp /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice /Users/gary/Applications/HiC-Pro-master/scripts; cd /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/; /Users/gary/anaconda/bin/python setup.py install --user;)
cp: /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice: Not a directory
/bin/sh: line 0: cd: /Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/: Not a directory
/Users/gary/anaconda/bin/python: can't open file 'setup.py': [Errno 2] No such file or directory
make: *** [iced] Error 2
Could you check if you this folder exists ;
/Users/gary/Applications/HiC-Pro-master/scripts/src/ice_mod/
If I remember correctly, in your previous trial, you made a mistake in the PREFIX, therefore asking HiC-Pro to be install within your downloaded directory. I'm just wondering if you did not remove some files when you did that.
I would advice, to start from scratch. Download a new version. Set the config-install file properly and try again ...
Nicolas
Yung-Chih Lai
Thanks a lot. On my notebook, iced-0.4.0 is a folder, but ice_mod is not a folder (the detail below). I try to remove the HiC-Pro, and download a new one from GitHub to re-install (the detail below). However, the same error message appeared again. Could you help me? Any other information I can provide to figure out this issue? Many thanks.
Best,
Gary
# There is a ice_mod on my Mac, but it is not a folder
gary > pwd
/Users/gary/Applications/HiC-Pro-master/scripts/src
gary > ll
total 88
-rwxr-xr-x@ 1 gary staff 30K Mar 2 01:16 build_matrix.cpp
-rwxr-xr-x@ 1 gary staff 4.1K Mar 2 01:16 cutsite_trimming.cpp
-rwxr-xr-x@ 1 gary staff 11B Mar 2 01:16 ice_mod
drwxr-xr-x@ 17 gary staff 578B Mar 2 01:16 iced-0.4.0/
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Victoria
$ make install
(g++ -Wall -O2 -std=c++0x -o build_matrix /Users/noekimv2/HiC-Pro-master/scripts/src/build_matrix.cpp; mv build_matrix /Users/noekimv2/HiC-Pro-master/scripts)
/Users/noekimv2/HiC-Pro-master/scripts/src/build_matrix.cpp:249:7: warning: private field
'idx' is not used [-Wunused-private-field]
int idx; // really needed ?
^
1 warning generated.
(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /Users/noekimv2/HiC-Pro-master/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /Users/noekimv2/HiC-Pro-master/scripts)
(cp /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice /Users/noekimv2/HiC-Pro-master/scripts; cd /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/; /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install --user;)
cp: /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice: Not a directory
/bin/sh: line 0: cd: /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/: Not a directory
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file 'setup.py': [Errno 2] No such file or directory
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Victoria
nservant
Let's try to fix it !
(cp /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice /Users/noekimv2/HiC-Pro-master/scripts; cd /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/; /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install --user;)
cp: /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice: Not a directory
/bin/sh: line 0: cd: /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/: Not a directory
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file 'setup.py': [Errno 2] No such file or directory
Thanks
Victoria
cp: /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/iced/scripts/ice: Not a directory
/bin/sh: line 0: cd: /Users/noekimv2/HiC-Pro-master/scripts/src/ice_mod/: Not a directory
The following is in the /scripts/src/ file which includes ice_mod not as a directory.
Ges-Mac-Pro:HiC-Pro-master $ cd scripts
Ges-Mac-Pro:scripts $ ls
Makefile* make_plots.sh* merge_stats.sh*
bowtie_combine.sh* make_sge_script.sh* merge_valid_interactions.sh*
bowtie_pairing.sh* make_slurm_script.sh* onTarget.py*
bowtie_wrap.sh* make_torque_script.sh* plot_hic_contacts.R*
build_matrix* mapped_2hic_dnase.py* plot_hic_fragment.R*
build_raw_maps.sh* mapped_2hic_fragments.py* plot_mapping_portion.R*
cutsite_trimming* mapped_2hic_fragments.sh* plot_pairing_portion.R*
hic.inc.sh* mapping_stat.sh* split_valid_interactions.py*
ice_norm.sh* markAllelicStatus.py* src/
install/ mergeSAM.py*
make_lsf_script.sh* merge_statfiles.py*
Ges-Mac-Pro:scripts$ cd src
Ges-Mac-Pro:src$ ls
build_matrix.cpp* ice_mod* iced-0.4.2/
cutsite_trimming.cpp* iced-0.4.0/
The following location did not have setup.py file in the folder as seen below:
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file 'setup.py': [Errno 2] No such file or directory
Ges-Mac-Pro:src $ cd /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/
Ges-Mac-Pro:MacOS $ ls
Python*
Please let know if you need more information.
Thank you!
Victoria
nservant
So it seems that the ice_mod symbolic link is there. I do not understand why it doesn't want to follow the link.
Anyway. Could you try to remove the ice_mod link, and to rename the folder iced-0.4.2/ into ice_mod ?
By doing this, you will remove the symbolink link which seems to promote the error ... or at least I hope so !
Victoria
Thanks so much. It went through! However, I think I am not able to use HiC-Pro command and at the end of installation it did not specify which folder it was installed in as seen below. I would appreciate your help with this.
nservant
Victoria
nservant
My understanding is that you are on '/Users/noekimv2/HiC-Pro-master', and you want to install HiCPro on '/Users/noekimv2/HiC-Pro_2.9.0'
Am I correct ?
Anyway it seems that the copy has been done. Could check if it was installed in '/Users/noekimv2/HiC-Pro_2.9.0 ?
Victoria
nservant
I think it is installed. Could you just show me what you have in the script folder ?
Victoria
...
nservant
As you are on Mac, I would adive two additional tests ;
Open python and just try
>> import iced
To be sure that the iced module was well installed.
Then, check you sort command. It should support the -V option.
Finally, I would strongly suggest to run the test dataset first, to be sure that everything is fine.
Victoria
nservant
Good luck !