Hello,
I am attempting to install HiC-Pro, but the installation step is failing. All dependencies are available (through a conda environment or a shared installation).
Installing the iced package in --user repository
(cp /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts/src/ice_mod/iced/scripts/ice /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts; cd /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts/src/ice_mod/; /sc/hydra/work/estilm01/Tools/anaconda2/envs/hic_py2/bin/python setup.py install --user;)
/sc/hydra/work/estilm01/Tools/anaconda2/envs/hic_py2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'
warnings.warn(msg)
/sc/hydra/work/estilm01/Tools/anaconda2/envs/hic_py2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'
warnings.warn(msg)
Warning: Assuming default configuration (iced/utils/{setup_utils,setup}.py was not found)Appending iced.utils configuration to iced
Ignoring attempt to set 'name' (from 'iced' to 'iced.utils')
Appending iced.datasets configuration to iced
Ignoring attempt to set 'name' (from 'iced' to 'iced.datasets')
non-existing path in 'iced/io': '../src/cblas'
non-existing path in 'iced/io': '../src/cblas'
Appending iced.io configuration to iced
Ignoring attempt to set 'name' (from 'iced' to 'iced.io')
non-existing path in 'iced': '../src/cblas'
non-existing path in 'iced': '../src/cblas'
Appending iced configuration to
Ignoring attempt to set 'name' (from '' to 'iced')
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
buildsrc
building extension "iced.io.fastio" sources
building extension "iced.io.read" sources
building extension "iced.normalization" sources
building extension "iced.filter" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running build_scripts
running install_lib
running install_scripts
changing mode of /hpc/users/estilm01/.local/bin/ice to 755
running install_data
running install_egg_info
Removing /hpc/users/estilm01/.local/lib/python2.7/site-packages/iced-0.4.2-py2.7.egg-info
Writing /hpc/users/estilm01/.local/lib/python2.7/site-packages/iced-0.4.2-py2.7.egg-info
running install_clib
customize UnixCCompiler
cp -Ri /sc/hydra/work/estilm01/Tools/HiC-Pro /sc/hydra/work/estilm01/Tools/HiC-Pro/HiC-Pro_2.11.1
cp: cannot copy a directory, ‘/sc/hydra/work/estilm01/Tools/HiC-Pro’, into itself, ‘/sc/hydra/work/estilm01/Tools/HiC-Pro/HiC-Pro_2.11.1/HiC-Pro’
make: *** [cp] Error 1
To attempt to circumvent this error, I manually copied the "scripts" from the main directory to the newly created "HiC-Pro_2.11.1" subdirectory. With that manual step, I was able to run the parallel step1 through the alignment steps, but the pipeline then fails at the mergeSAM step. This failure to merge the R1 and R2 tags was replicated with the provided test dataset and a personal dataset.
mergeSAM error:
Thu Feb 6 10:46:16 EST 2020
Pairing of R1 and R2 tags ...
Logs: logs/dixon_2M_2/mergeSAM.log
make: *** [bowtie_pairing] Error 1
Any insight into why the 'make install' step is failing is much appreciated.
Hello, I am attempting to install HiC-Pro, but the installation step is failing. All dependencies are available (through a conda environment or a shared installation).
Here is the installation error:
(hic_py2) [estilm01@li03c03 HiC-Pro]$ make CONFIG_SYS=config-install.txt install (g++ -Wall -O2 -std=c++0x -o build_matrix /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts/src/build_matrix.cpp; mv build_matrix /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts) (g++ -Wall -O2 -std=c++0x -o cutsite_trimming /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts) runner=estilm01
Installing the iced package in --user repository (cp /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts/src/ice_mod/iced/scripts/ice /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts; cd /sc/hydra/work/estilm01/Tools/HiC-Pro/scripts/src/ice_mod/; /sc/hydra/work/estilm01/Tools/anaconda2/envs/hic_py2/bin/python setup.py install --user;) /sc/hydra/work/estilm01/Tools/anaconda2/envs/hic_py2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data' warnings.warn(msg) /sc/hydra/work/estilm01/Tools/anaconda2/envs/hic_py2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe' warnings.warn(msg) Warning: Assuming default configuration (iced/utils/{setup_utils,setup}.py was not found)Appending iced.utils configuration to iced Ignoring attempt to set 'name' (from 'iced' to 'iced.utils') Appending iced.datasets configuration to iced Ignoring attempt to set 'name' (from 'iced' to 'iced.datasets') non-existing path in 'iced/io': '../src/cblas' non-existing path in 'iced/io': '../src/cblas' Appending iced.io configuration to iced Ignoring attempt to set 'name' (from 'iced' to 'iced.io') non-existing path in 'iced': '../src/cblas' non-existing path in 'iced': '../src/cblas' Appending iced configuration to Ignoring attempt to set 'name' (from '' to 'iced') running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src buildsrc building extension "iced.io.fastio" sources building extension "iced.io.read" sources building extension "iced.normalization" sources building extension "iced.filter" sources building data_files sources build_src: building npy-pkg config files running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running build_scripts running install_lib running install_scripts changing mode of /hpc/users/estilm01/.local/bin/ice to 755 running install_data running install_egg_info Removing /hpc/users/estilm01/.local/lib/python2.7/site-packages/iced-0.4.2-py2.7.egg-info Writing /hpc/users/estilm01/.local/lib/python2.7/site-packages/iced-0.4.2-py2.7.egg-info running install_clib customize UnixCCompiler cp -Ri /sc/hydra/work/estilm01/Tools/HiC-Pro /sc/hydra/work/estilm01/Tools/HiC-Pro/HiC-Pro_2.11.1 cp: cannot copy a directory, ‘/sc/hydra/work/estilm01/Tools/HiC-Pro’, into itself, ‘/sc/hydra/work/estilm01/Tools/HiC-Pro/HiC-Pro_2.11.1/HiC-Pro’ make: *** [cp] Error 1
To attempt to circumvent this error, I manually copied the "scripts" from the main directory to the newly created "HiC-Pro_2.11.1" subdirectory. With that manual step, I was able to run the parallel step1 through the alignment steps, but the pipeline then fails at the mergeSAM step. This failure to merge the R1 and R2 tags was replicated with the provided test dataset and a personal dataset.
mergeSAM error:
Thu Feb 6 10:46:16 EST 2020 Pairing of R1 and R2 tags ... Logs: logs/dixon_2M_2/mergeSAM.log make: *** [bowtie_pairing] Error 1
Any insight into why the 'make install' step is failing is much appreciated.
Best, Molly