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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Urgent: Installation Issue #374

Closed sanchari24 closed 3 years ago

sanchari24 commented 4 years ago

Hello, I have been trying to install HiC-Pro past couple of days, but no luck and have lost too much time. I am working in a cluster environment, and was trying to install it for my environment. I keep getting an error for the Test data on Human: make: *** No targets. Stop.

I have provided the logs and the config file info. Will be very very grateful for some insights. Thanks

config-system.txt

R_PATH = /opt/share/Debian-Buster/CRAN-R/R-3.6.2/bin BOWTIE2_PATH = /opt/share/Linux_x86_64/bowtie2/bowtie2-2.3.4.1 SAMTOOLS_PATH = /opt/share/Debian-Buster/samtools-1.9/bin PYTHON_PATH = /usr/bin INSTALL_PATH = /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4 SCRIPTS = /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4/scripts SOURCES = /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4/scripts/src ANNOT_DIR = /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4/annotation CLUSTER_SCRIPT = /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4/scripts/make_torque_script.sh

ssircar@node9:~/HiC-Pro$ make configure

make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt make[1]: Entering directory '/ips2/users/ssircar/cluster/HiC-Pro' ./scripts/install/install_dependencies.sh -c ./config-install.txt -o  /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4 -q Make sure internet connection works for your shell prompt under current user's privilege ... Starting HiC-Pro installation ... 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.

make[1]: Leaving directory '/ips2/users/ssircar/cluster/HiC-Pro'

ssircar@node9:~/HiC-Pro$ make install

(g++ -Wall -O2 -std=c++0x -o build_matrix /ips2/users/ssircar/cluster/HiC-Pro/scripts/src/build_matrix.cpp; mv build_matrix /ips2/users/ssircar/cluster/HiC-Pro/scripts) (g++ -Wall -O2 -std=c++0x -o cutsite_trimming /ips2/users/ssircar/cluster/HiC-Pro/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /ips2/users/ssircar/cluster/HiC-Pro/scripts) Installing the iced package in --user repository [runner=ssircar] (cd /ips2/users/ssircar/cluster/HiC-Pro/scripts/src/ice_mod/; /usr/bin/python setup.py install --user;) /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'   warnings.warn(msg) /usr/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 creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/iced copying iced/normalization.py -> build/lib.linux-x86_64-2.7/iced copying iced/filter.py -> build/lib.linux-x86_64-2.7/iced copying iced/setup.py -> build/lib.linux-x86_64-2.7/iced copying iced/init.py -> build/lib.linux-x86_64-2.7/iced creating build/lib.linux-x86_64-2.7/iced/utils copying iced/utils/_genome.py -> build/lib.linux-x86_64-2.7/iced/utils copying iced/utils/_validation.py -> build/lib.linux-x86_64-2.7/iced/utils copying iced/utils/validation.py -> build/lib.linux-x86_64-2.7/iced/utils copying iced/utils/init.py -> build/lib.linux-x86_64-2.7/iced/utils creating build/lib.linux-x86_64-2.7/iced/datasets copying iced/datasets/setup.py -> build/lib.linux-x86_64-2.7/iced/datasets copying iced/datasets/base.py -> build/lib.linux-x86_64-2.7/iced/datasets copying iced/datasets/init.py -> build/lib.linux-x86_64-2.7/iced/datasets creating build/lib.linux-x86_64-2.7/iced/io copying iced/io/_io_else.py -> build/lib.linux-x86_64-2.7/iced/io copying iced/io/setup.py -> build/lib.linux-x86_64-2.7/iced/io copying iced/io/_io_pandas.py -> build/lib.linux-x86_64-2.7/iced/io copying iced/io/init.py -> build/lib.linux-x86_64-2.7/iced/io running build_ext customize UnixCCompiler customize UnixCCompiler using buildext building 'iced.io.fastio' extension compiling C sources C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC

creating build/temp.linux-x86_64-2.7/iced creating build/temp.linux-x86_64-2.7/iced/io compile options: '-I../src/cblas -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c' x8664-linux-gnu-gcc: iced/io/fastio.c In file included from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,                  from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,                  from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,                  from iced/io/fastio_.c:435: /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]  #warning "Using deprecated NumPy API, disable it with " \   ^~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x8664-2.7/iced/io/fastio.o -lm -o build/lib.linux-x8664-2.7/iced/io/fastio.so building 'iced.io.read' extension compiling C sources C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-I../src/cblas -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c' x86_64-linux-gnu-gcc: iced/io/read.c x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/iced/io/read.o -lm -o build/lib.linux-x86_64-2.7/iced/io/read.so building 'iced.normalization' extension compiling C sources C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-I../src/cblas -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c' x86_64-linux-gnu-gcc: iced/normalization.c In file included from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,                  from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,                  from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,                  from iced/normalization.c:435: /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]  #warning "Using deprecated NumPy API, disable it with " \   ^~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/iced/normalization.o -lm -o build/lib.linux-x86_64-2.7/iced/normalization.so building 'iced.filter' extension compiling C sources C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-I../src/cblas -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c' x86_64-linux-gnu-gcc: iced/filter.c In file included from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,                  from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,                  from /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,                  from iced/filter.c:435: /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]  #warning "Using deprecated NumPy API, disable it with " \   ^~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/iced/filter.o -lm -o build/lib.linux-x86_64-2.7/iced/filter.so running build_scripts creating build/scripts.linux-x86_64-2.7 copying and adjusting iced/scripts/ice -> build/scripts.linux-x86_64-2.7 running install_lib copying build/lib.linux-x86_64-2.7/iced/io/read.so -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io copying build/lib.linux-x8664-2.7/iced/io/fastio.so -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io copying build/lib.linux-x86_64-2.7/iced/io/_io_else.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io copying build/lib.linux-x86_64-2.7/iced/io/setup.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io copying build/lib.linux-x86_64-2.7/iced/io/_io_pandas.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io copying build/lib.linux-x86_64-2.7/iced/io/init.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io copying build/lib.linux-x86_64-2.7/iced/utils/_genome.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils copying build/lib.linux-x86_64-2.7/iced/utils/_validation.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils copying build/lib.linux-x86_64-2.7/iced/utils/validation.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils copying build/lib.linux-x86_64-2.7/iced/utils/init.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils copying build/lib.linux-x86_64-2.7/iced/normalization.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced copying build/lib.linux-x86_64-2.7/iced/filter.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced copying build/lib.linux-x86_64-2.7/iced/filter.so -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced copying build/lib.linux-x86_64-2.7/iced/setup.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced copying build/lib.linux-x86_64-2.7/iced/datasets/setup.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets copying build/lib.linux-x86_64-2.7/iced/datasets/base.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets copying build/lib.linux-x86_64-2.7/iced/datasets/init.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets copying build/lib.linux-x86_64-2.7/iced/normalization.so -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced copying build/lib.linux-x86_64-2.7/iced/init.py -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io/_io_else.py to _io_else.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io/setup.py to setup.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io/_io_pandas.py to _io_pandas.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/io/init.py to init.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils/_genome.py to _genome.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils/_validation.py to _validation.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils/validation.py to validation.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/utils/init.py to init.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/normalization.py to normalization.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/filter.py to filter.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/setup.py to setup.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets/setup.py to setup.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets/base.py to base.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets/init.py to init.pyc byte-compiling /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/init.py to init.pyc running install_scripts copying build/scripts.linux-x86_64-2.7/ice -> /ips2/users/ssircar/cluster/.local/bin changing mode of /ips2/users/ssircar/cluster/.local/bin/ice to 777 running install_data copying iced/datasets/data/duan2009/duan.SC.10000.raw_sub.matrix -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets/data/duan2009 copying iced/datasets/data/duan2009/duan.SC.10000.raw_sub.bed -> /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced/datasets/data/duan2009 running install_egg_info Removing /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced-0.4.2.egg-info Writing /ips2/users/ssircar/cluster/.local/lib/python2.7/site-packages/iced-0.4.2.egg-info running install_clib customize UnixCCompiler cp -Ri /ips2/users/ssircar/cluster/HiC-Pro /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4 HiC-Pro installed in /ips2/users/ssircar/cluster/.local/bin/HiC-Pro_2.11.4 !

HiC-Pro config file:

TMP_DIR = tmp LOGS_DIR = logs BOWTIE2_OUTPUT_DIR = bowtie_results MAPC_OUTPUT = hic_results RAW_DIR = rawdata

ssircar@node9:~/.local/bin/HiC-Pro_2.11.4/bin$ workingDir="/NetScratch/sanchari/hicpro_test"

ssircar@node9:~/.local/bin/HiC-Pro_2.11.4/bin$ ./HiC-Pro -i $workingDir/HiCPro_testdata/test_data -o $workingDir/out_put_test_data -c $workingDir/hicpro_config.txt

**make: * No targets.  Stop.

nservant commented 4 years ago

not sure to see what's going wrong. The only thing I can tell you is that this is usually not a good idea to work on the installation folder ... Does it chang something if you call HiC-pro using its full path ?

liwang0307 commented 2 years ago

Hi, I have the exact same issue. How did you solve it? Thanks, @sanchari24