pb-cdunn
commented
5 years ago Sorry. The code here is way out of date. Please use Bioconda. conda install pb-assembly
Closed YuanwenGuo closed 5 years ago
pb-cdunn
commented
5 years ago Sorry. The code here is way out of date. Please use Bioconda. conda install pb-assembly
Dear developers,
I am trying to install Falcon on slurm system. I followed the commands in "The easy way" to install, but it failed after the "make -j all" step and showed log information below:
make -C ./FALCON-make/ all make[1]: Entering directory
/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' make show make[2]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' mkdir -p /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin which python /opt/software/software/Python/2.7.15-foss-2018b/bin/python echo "PYTHONUSERBASE=/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env" PYTHONUSERBASE=/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env python -c 'import site; print site.USER_BASE' /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env echo "FALCON_PIP_EDIT=--edit" FALCON_PIP_EDIT=--edit echo "FALCON_PIP_USER=--user" FALCON_PIP_USER=--user make[2]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' make install-pip make[2]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' python -c 'import pip; print pip' || python get-pip.py --user <module 'pip' from '/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/pip/init.pyc'> pip install --user --upgrade pip DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Requirement already up-to-date: pip in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (19.1.1) pip install --user --upgrade setuptools # needed when --edit is used DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Requirement already up-to-date: setuptools in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (41.0.1) pip install --user nose pytest # for running tests while building DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Requirement already satisfied: nose in /opt/software/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/nose-1.3.7-py2.7.egg (1.3.7) Requirement already satisfied: pytest in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (4.5.0) Requirement already satisfied: funcsigs>=1.0; python_version < "3.0" in /opt/software/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/funcsigs-1.0.2-py2.7.egg (from pytest) (1.0.2) Requirement already satisfied: py>=1.5.0 in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (1.8.0) Requirement already satisfied: pluggy!=0.10,<1.0,>=0.9 in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (0.11.0) Requirement already satisfied: six>=1.10.0 in /opt/software/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/six-1.11.0-py2.7.egg (from pytest) (1.11.0) Requirement already satisfied: pathlib2>=2.2.0; python_version < "3.6" in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (2.3.3) Requirement already satisfied: atomicwrites>=1.0 in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (1.3.0) Requirement already satisfied: wcwidth in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (0.1.7) Requirement already satisfied: more-itertools<6.0.0,>=4.0.0; python_version <= "2.7" in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (5.0.0) Requirement already satisfied: attrs>=17.4.0 in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (19.1.0) Requirement already satisfied: setuptools in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest) (41.0.1) Requirement already satisfied: scandir; python_version < "3.5" in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pathlib2>=2.2.0; python_version < "3.6"->pytest) (1.10.0) make[2]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' make install # This will double -D_GNU_SOURCE, but that is ok for now. make[2]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB all make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER all make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR all cd /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW; pip uninstall -v .; pip install -v --user --edit .TODO: copy vs. symlink?
make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/nim-falcon/src -j1 all make[3]: Entering directory
/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER' make[3]: Nothing to be done forall'. make[3]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER' PREFIX=/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER symlink make[3]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR' make[3]: Nothing to be done forall'. make[3]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR' PREFIX=/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR symlink ln -sf /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/git-sym/git-sym /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin/git-sym make[3]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/nim-falcon/src' make[3]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB' nim --threads:on --threadAnalysis:off --verbosity:2 -d:release --tlsemulation:on --out:fc_rr_hctg_track2.exe c fc_rr_hctg_track2.nim make[3]: Nothing to be done forall'. make[3]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB' PREFIX=/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env make -C /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB symlink make[3]: nim: Command not found make[3]: [fc_rr_hctg_track2.exe] Error 127 make[3]: Leaving directory `/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/nim-falcon/src' make[2]: [install-nim-falcon] Error 2 make[2]: *** Waiting for unfinished jobs.... make[3]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER' ln -sf /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER/datander /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER/TANmask /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER/REPmask /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER/HPC.TANmask /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER/HPC.REPmask /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin make[3]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR' ln -sf /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR/dexta /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR/undexta /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin make[3]: Entering directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB' ln -sf /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/fasta2DB /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DB2fasta /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DBsplit /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DBdust /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/Catrack /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DBshow /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DBstats /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DBrm /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/simulator /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/fasta2DAM /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DAM2fasta /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DBdump /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/rangen /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin make[3]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DEXTRACTOR' make[3]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAMASKER' ln -sf /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/libdazzdb.a /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib ln -sf /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/QV.h /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB/DB.h /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/include make[3]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/DAZZ_DB' DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. ERROR: You must give at least one requirement to uninstall (see "pip help uninstall") Exception information: Traceback (most recent call last): File "/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/pip/_internal/cli/base_command.py", line 178, in main status = self.run(options, args) File "/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/pip/_internal/commands/uninstall.py", line 66, in run '"pip help %(name)s")' % dict(name=self.name) InstallationError: You must give at least one requirement to uninstall (see "pip help uninstall") DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Created temporary directory: /tmp/pip-ephem-wheel-cache-_4bQpE Created temporary directory: /tmp/pip-req-tracker-oUXCOG Created requirements tracker '/tmp/pip-req-tracker-oUXCOG' Created temporary directory: /tmp/pip-install-lseXmV Obtaining file:///bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW Added file:///bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW to build tracker '/tmp/pip-req-tracker-oUXCOG' Running setup.py (path:/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW/setup.py) egg_info for package from file:///bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW Running command python setup.py egg_info /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/setuptools/dist.py:472: UserWarning: Normalizing '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef ' to '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef' normalized_version, running egg_info writing requirements to pypeflow.egg-info/requires.txt writing pypeflow.egg-info/PKG-INFO writing top-level names to pypeflow.egg-info/top_level.txt writing dependency_links to pypeflow.egg-info/dependency_links.txt writing entry points to pypeflow.egg-info/entry_points.txt reading manifest file 'pypeflow.egg-info/SOURCES.txt' writing manifest file 'pypeflow.egg-info/SOURCES.txt' Source in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW has version 2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef, which satisfies requirement pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef from file:///bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW Removed pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef from file:///bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW from build tracker '/tmp/pip-req-tracker-oUXCOG' Requirement already satisfied: networkx<=1.11,>=1.7 in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef) (1.11) Requirement already satisfied: future>=0.16.0 in /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef) (0.17.1) Requirement already satisfied: decorator>=3.4.0 in /opt/software/software/Python/2.7.15-foss-2018b/lib/python2.7/site-packages/decorator-4.3.0-py2.7.egg (from networkx<=1.11,>=1.7->pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef) (4.3.0) Installing collected packages: pypeflow Found existing installation: pypeflow 2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef Uninstalling pypeflow-2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef: Created temporary directory: /tmp/pip-uninstall-BXbaN3 Removing file or directory /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow.egg-link Removing pth entries from /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/easy-install.pth: Removing entry: /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW Successfully uninstalled pypeflow-2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef Running setup.py develop for pypeflow Running command /opt/software/software/Python/2.7.15-foss-2018b/bin/python -c 'import setuptools, tokenize;file='"'"'/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/pypeFLOW/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' develop --no-deps --user --prefix= /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/setuptools/dist.py:472: UserWarning: Normalizing '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef ' to '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef' normalized_version, running develop running egg_info writing requirements to pypeflow.egg-info/requires.txt writing pypeflow.egg-info/PKG-INFO writing top-level names to pypeflow.egg-info/top_level.txt writing dependency_links to pypeflow.egg-info/dependency_links.txt writing entry points to pypeflow.egg-info/entry_points.txt reading manifest file 'pypeflow.egg-info/SOURCES.txt' writing manifest file 'pypeflow.egg-info/SOURCES.txt' running build_ext Creating /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow.egg-link (link to .) Adding pypeflow 2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef to easy-install.pth file Installing pwatcher-pypeflow-example script to /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin Installing heartbeat-wrapper script to /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/bin Installing pwatcher-main script to /bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/fc_env/binSuccessfully installed pypeflow Cleaning up... Removed build tracker '/tmp/pip-req-tracker-oUXCOG' make[2]: Leaving directory
/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' make[1]: *** [all] Error 2 make[1]: Leaving directory/bulk/yuanwen/Tools_new/FALCON/FALCON-integrate/FALCON-make' make: *** [all] Error 2I am using python module 2.7.15 by "module load Python/2.7.15-foss-2018b"
Could you please help me with this issue? Thank you!
Best, Yuanwen