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nanoporetech / pomoxis

Analysis components from Oxford Nanopore Research
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installation error - porechop #25

Closed mjfi2sb3 closed 5 years ago

mjfi2sb3 commented 5 years ago

Hi,

I am getting the following error related to porechop while compiling. Any suggestions how to resolve?

Processing dependencies for pomoxis==0.2.0 Searching for Porechop Reading https://pypi.org/simple/Porechop/ Couldn't find index page for 'Porechop' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading https://pypi.org/simple/ No local packages or working download links found for Porechop error: Could not find suitable distribution for Requirement.parse('Porechop') make: *** [install] Error 1

cjw85 commented 5 years ago

Hi @mjfi2sb3,

Can you provide the command you are running to install pomoxis? Porechop is indeed not available on pypi, though the installation methods in the README.md (bar the last one if run as-is), should not cause an attempt to be made.

If you are a conda user you will most likely wish to follow the instructions under "Installation with conda", if not the instructions under "Installation from source" will be more appropriate.

mjfi2sb3 commented 5 years ago

Hi @cjw85,

I actually tried "Installation with conda" (CONDA=/path/to/anaconda3 make conda) and "Installation from source" (make install). Both gave the same error.

Best, /SB

On Mon, 7 Jan 2019 at 11:59, cjw85 notifications@github.com wrote:

Hi @mjfi2sb3 https://github.com/mjfi2sb3,

Can you provide the command you are running to install pomoxis? Porechop is indeed not available on pypi, though the installation methods in the README.md (bar the last one if run as-is), should not cause an attempt to be made.

If you are a conda user you will most likely wish to follow the instructions under "Installation with conda", if not the instructions under "Installation from source" will be more appropriate.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nanoporetech/pomoxis/issues/25#issuecomment-451865080, or mute the thread https://github.com/notifications/unsubscribe-auth/APR8U08AR_nKSoONulJL0P_nMm6tJFKtks5vAwxfgaJpZM4Zy_Ee .

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cjw85 commented 5 years ago

The conda route would install Porechop using conda, so I am puzzled as to how you would get the above error message. Can you attach the full terminal output, perhaps something is going wrong earlier on?

mjfi2sb3 commented 5 years ago

Hi,

The command I run is

CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make install

and the log is attached.

Best & thanks, /SB

On Mon, 7 Jan 2019 at 12:08, cjw85 notifications@github.com wrote:

The conda route would install Porechop using conda, so I am puzzled as to how you would get the above error message. Can you attach the full terminal output, perhaps something is going wrong earlier on?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nanoporetech/pomoxis/issues/25#issuecomment-451867313, or mute the thread https://github.com/notifications/unsubscribe-auth/APR8U4w7thzReDsymXkxtaEFtR5cOFFIks5vAw5zgaJpZM4Zy_Ee .

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cd submodules/bwapy && make bwa/libbwa.a make[1]: Entering directory /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/submodules/bwapy' make[1]:bwa/libbwa.a' is up to date. make[1]: Leaving directory `/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/submodules/bwapy' . ./venv/bin/activate && cd submodules/bwapy && python setup.py install running install running bdist_egg running egg_info writing bwapy.egg-info/PKG-INFO writing dependency_links to bwapy.egg-info/dependency_links.txt writing entry points to bwapy.egg-info/entry_points.txt writing requirements to bwapy.egg-info/requires.txt writing top-level names to bwapy.egg-info/top_level.txt reading manifest file 'bwapy.egg-info/SOURCES.txt' writing manifest file 'bwapy.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py running build_ext creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/bwapy copying build/lib.linux-x86_64-3.7/bwapy/init.py -> build/bdist.linux-x86_64/egg/bwapy copying build/lib.linux-x86_64-3.7/bwapy/libbwa.py -> build/bdist.linux-x86_64/egg/bwapy copying build/lib.linux-x86_64-3.7/bwalib.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg byte-compiling build/bdist.linux-x86_64/egg/bwapy/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/bwapy/libbwa.py to libbwa.cpython-37.pyc creating stub loader for bwalib.cpython-37m-x86_64-linux-gnu.so byte-compiling build/bdist.linux-x86_64/egg/bwalib.py to bwalib.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bwapy.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt creating 'dist/bwapy-0.1.3-py3.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing bwapy-0.1.3-py3.7-linux-x86_64.egg removing '/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/bwapy-0.1.3-py3.7-linux-x86_64.egg' (and everything under it) creating /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/bwapy-0.1.3-py3.7-linux-x86_64.egg Extracting bwapy-0.1.3-py3.7-linux-x86_64.egg to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages bwapy 0.1.3 is already the active version in easy-install.pth Installing bwamempy script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin

Installed /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/bwapy-0.1.3-py3.7-linux-x86_64.egg Processing dependencies for bwapy==0.1.3 Searching for cffi==1.11.5 Best match: cffi 1.11.5 Adding cffi 1.11.5 to easy-install.pth file

Using /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages Searching for pycparser==2.19 Best match: pycparser 2.19 Adding pycparser 2.19 to easy-install.pth file

Using /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages Finished processing dependencies for bwapy==0.1.3 . ./venv/bin/activate && POMO_BINARIES=1 python setup.py install running install running bdist_egg running egg_info writing pomoxis.egg-info/PKG-INFO writing dependency_links to pomoxis.egg-info/dependency_links.txt writing entry points to pomoxis.egg-info/entry_points.txt writing requirements to pomoxis.egg-info/requires.txt writing top-level names to pomoxis.egg-info/top_level.txt reading manifest file 'pomoxis.egg-info/SOURCES.txt' writing manifest file 'pomoxis.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/pomoxis copying build/lib/pomoxis/init.py -> build/bdist.linux-x86_64/egg/pomoxis copying build/lib/pomoxis/watcher.py -> build/bdist.linux-x86_64/egg/pomoxis creating build/bdist.linux-x86_64/egg/pomoxis/align copying build/lib/pomoxis/align/init.py -> build/bdist.linux-x86_64/egg/pomoxis/align copying build/lib/pomoxis/align/bwa.py -> build/bdist.linux-x86_64/egg/pomoxis/align copying build/lib/pomoxis/align/common.py -> build/bdist.linux-x86_64/egg/pomoxis/align copying build/lib/pomoxis/align/minimap.py -> build/bdist.linux-x86_64/egg/pomoxis/align copying build/lib/pomoxis/align/py2client.py -> build/bdist.linux-x86_64/egg/pomoxis/align creating build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/init.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/bio.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/catalogue_errors.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/common_errors_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/coverage_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/qscores_from_summary.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/ref_seqs_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/simulate_calls.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/stats_from_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/subsample_bam.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/summary_from_stats.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/trim_alignments.py -> build/bdist.linux-x86_64/egg/pomoxis/common copying build/lib/pomoxis/common/util.py -> build/bdist.linux-x86_64/egg/pomoxis/common creating build/bdist.linux-x86_64/egg/pomoxis/provider copying build/lib/pomoxis/provider/init.py -> build/bdist.linux-x86_64/egg/pomoxis/provider copying build/lib/pomoxis/provider/replayfast5.py -> build/bdist.linux-x86_64/egg/pomoxis/provider byte-compiling build/bdist.linux-x86_64/egg/pomoxis/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/watcher.py to watcher.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/bwa.py to bwa.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/common.py to common.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/minimap.py to minimap.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/align/py2client.py to py2client.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/bio.py to bio.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/catalogue_errors.py to catalogue_errors.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/common_errors_from_bam.py to common_errors_from_bam.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/coverage_from_bam.py to coverage_from_bam.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/qscores_from_summary.py to qscores_from_summary.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/ref_seqs_from_bam.py to ref_seqs_from_bam.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/simulate_calls.py to simulate_calls.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/stats_from_bam.py to stats_from_bam.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/subsample_bam.py to subsample_bam.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/summary_from_stats.py to summary_from_stats.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/trim_alignments.py to trim_alignments.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/common/util.py to util.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/provider/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/pomoxis/provider/replayfast5.py to replayfast5.cpython-37.pyc installing package data to build/bdist.linux-x86_64/egg running install_data creating build/bdist.linux-x86_64/egg/exes copying bincache/minimap2 -> build/bdist.linux-x86_64/egg/exes copying bincache/miniasm -> build/bdist.linux-x86_64/egg/exes copying bincache/racon -> build/bdist.linux-x86_64/egg/exes copying bincache/samtools -> build/bdist.linux-x86_64/egg/exes copying bincache/bcftools -> build/bdist.linux-x86_64/egg/exes copying bincache/seqkit -> build/bdist.linux-x86_64/egg/exes creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.7/assess_assembly -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.7/intersect_assembly_errors -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.7/mini_align -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.7/mini_assemble -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/assess_assembly to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/intersect_assembly_errors to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/mini_align to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/mini_assemble to 755 copying pomoxis.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying pomoxis.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pomoxis.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pomoxis.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pomoxis.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying pomoxis.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pomoxis.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating 'dist/pomoxis-0.2.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing pomoxis-0.2.0-py3.7.egg removing '/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg' (and everything under it) creating /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg Extracting pomoxis-0.2.0-py3.7.egg to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages pomoxis 0.2.0 is already the active version in easy-install.pth Installing assess_assembly script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing intersect_assembly_errors script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing mini_align script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing mini_assemble script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing align_serve script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing catalogue_errors script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing common_errors_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing coverage_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing coverage_from_fastx script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing fast_convert script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing long_fastx script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing pomoxis_path script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing qscores_from_summary script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing read_until_filter script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing ref_seqs_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing simulate_calls script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing split_fastx script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing stats_from_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing subsample_bam script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing summary_from_stats script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin Installing trim_alignments script to /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/bin

Installed /bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg Processing dependencies for pomoxis==0.2.0 Searching for Porechop Reading https://pypi.org/simple/Porechop/ File "build/bdist.linux-x86_64/egg/pomoxis/init.py", line 20 asyncio.async(wakeup()) ^ SyntaxError: invalid syntax

File "build/bdist.linux-x86_64/egg/pomoxis/watcher.py", line 85 self._loop.call_soon_threadsafe(asyncio.async, self._process_file(event)) ^ SyntaxError: invalid syntax

File "/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg/pomoxis/init.py", line 20 asyncio.async(wakeup()) ^ SyntaxError: invalid syntax

File "/bcl-nas/apps/pomoxis-v0.2.0-git1c2032c_02/venv/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg/pomoxis/watcher.py", line 85 self._loop.call_soon_threadsafe(asyncio.async, self._process_file(event)) ^ SyntaxError: invalid syntax

Couldn't find index page for 'Porechop' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading https://pypi.org/simple/ No local packages or working download links found for Porechop error: Could not find suitable distribution for Requirement.parse('Porechop') make: *** [install] Error 1

cjw85 commented 5 years ago

I think the command you want to be running is:

CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make conda

(I can see there is a typo in the README which we will correct). You are using python3.7, with which we do not test; you can see some errors in the log which pertain to this, though I doubt they are the cause of the Porechop issue.

mjfi2sb3 commented 5 years ago

Hi,

It seems that you are right CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make conda is the command I should have used (see attached log). However, when I run some of the commands such as trim_alignments -h I get the following error. Is this due to the python version?

` trim_alignments -h Traceback (most recent call last): File "/bcl-nas/apps/anaconda3/v2018.12/bin/trim_alignments", line 11, in

load_entry_point('pomoxis==0.2.0', 'console_scripts', 'trim_alignments')() File "/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py", line 487, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2728, in load_entry_point return ep.load() File "/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2346, in load return self.resolve() File "/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2352, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/bcl-nas/apps/anaconda3/v2018.12/lib/python3.7/site-packages/pomoxis-0.2.0-py3.7.egg/pomoxis/__init__.py", line 20 asyncio.async(wakeup()) ^ SyntaxError: invalid syntax ` Best, /SB -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. CONDA=/bcl-nas/apps/anaconda3/v2018.12/ make conda . /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda remove -n pomoxis --all Remove all packages in environment /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis: ## Package Plan ## environment location: /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis The following packages will be REMOVED: bcftools: 1.7-0 bioconda bzip2: 1.0.6-h470a237_2 conda-forge ca-certificates: 2018.11.29-ha4d7672_0 conda-forge certifi: 2018.11.29-py36_1000 conda-forge curl: 7.63.0-h74213dd_0 conda-forge krb5: 1.16.2-hbb41f41_0 conda-forge libcurl: 7.63.0-hbdb9355_0 conda-forge libdeflate: 1.0-h470a237_0 bioconda libedit: 3.1.20170329-0 conda-forge libffi: 3.2.1-hfc679d8_5 conda-forge libgcc: 7.2.0-h69d50b8_2 conda-forge libgcc-ng: 8.2.0-hdf63c60_1 libssh2: 1.8.0-h5b517e9_3 conda-forge libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge miniasm: 0.3_r179-ha92aebf_0 bioconda minimap2: 2.14-ha92aebf_0 bioconda ncurses: 5.9-10 conda-forge openssl: 1.0.2p-h470a237_2 conda-forge pigz: 2.3.4-0 conda-forge pip: 18.1-py36_1000 conda-forge porechop: 0.2.3_seqan2.1.1-py36h2d50403_3 bioconda python: 3.6.6-h5001a0f_3 conda-forge racon: 1.3.1-he941832_5 bioconda readline: 7.0-0 conda-forge samtools: 1.8-h46bd0b3_5 bioconda seqkit: 0.8.0-2 bioconda setuptools: 40.6.3-py36_0 conda-forge sqlite: 3.26.0-h7b6447c_0 tk: 8.6.9-ha92aebf_0 conda-forge wheel: 0.32.3-py36_0 conda-forge xz: 5.2.4-h470a237_1 conda-forge zlib: 1.2.11-h470a237_3 conda-forge Proceed ([y]/n)? y . /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda create -y -n pomoxis -c bioconda -c conda-forge porechop \ samtools=1.8 bcftools=1.7 seqkit=0.8.0 \ miniasm=0.3 minimap2=2.14 racon=1.3.1 \ python=3.6 Solving environment: done ## Package Plan ## environment location: /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis added / updated specs: - bcftools=1.7 - miniasm=0.3 - minimap2=2.14 - porechop - python=3.6 - racon=1.3.1 - samtools=1.8 - seqkit=0.8.0 The following NEW packages will be INSTALLED: bcftools: 1.7-0 bioconda bzip2: 1.0.6-h470a237_2 conda-forge ca-certificates: 2018.11.29-ha4d7672_0 conda-forge certifi: 2018.11.29-py36_1000 conda-forge curl: 7.63.0-h74213dd_0 conda-forge krb5: 1.16.2-hbb41f41_0 conda-forge libcurl: 7.63.0-hbdb9355_0 conda-forge libdeflate: 1.0-h470a237_0 bioconda libedit: 3.1.20170329-0 conda-forge libffi: 3.2.1-hfc679d8_5 conda-forge libgcc: 7.2.0-h69d50b8_2 conda-forge libgcc-ng: 8.2.0-hdf63c60_1 libssh2: 1.8.0-h5b517e9_3 conda-forge libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge miniasm: 0.3_r179-ha92aebf_0 bioconda minimap2: 2.14-ha92aebf_0 bioconda ncurses: 5.9-10 conda-forge openssl: 1.0.2p-h470a237_2 conda-forge pigz: 2.3.4-0 conda-forge pip: 18.1-py36_1000 conda-forge porechop: 0.2.3_seqan2.1.1-py36h2d50403_3 bioconda python: 3.6.6-h5001a0f_3 conda-forge racon: 1.3.1-he941832_5 bioconda readline: 7.0-0 conda-forge samtools: 1.8-h46bd0b3_5 bioconda seqkit: 0.8.0-2 bioconda setuptools: 40.6.3-py36_0 conda-forge sqlite: 3.26.0-h7b6447c_0 tk: 8.6.9-ha92aebf_0 conda-forge wheel: 0.32.3-py36_0 conda-forge xz: 5.2.4-h470a237_1 conda-forge zlib: 1.2.11-h470a237_3 conda-forge Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate pomoxis # # To deactivate an active environment, use # # $ conda deactivate grep -v Porechop requirements.txt > conda_reqs.txt . /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda activate pomoxis && pip install -r conda_reqs.txt Collecting aiozmq (from -r conda_reqs.txt (line 3)) Using cached https://files.pythonhosted.org/packages/c8/5b/4ce8584fcd676664ba43170d9871ae177837fa72f59c08766bc0c589e177/aiozmq-0.7.1-py3-none-any.whl Collecting biopython>=1.63 (from -r conda_reqs.txt (line 4)) Using cached https://files.pythonhosted.org/packages/28/15/8ac646ff24cfa2588b4d5e5ea51e8d13f3d35806bd9498fbf40ef79026fd/biopython-1.73-cp36-cp36m-manylinux1_x86_64.whl Collecting cffi (from -r conda_reqs.txt (line 5)) Using cached https://files.pythonhosted.org/packages/6d/c0/47db8f624f3e4e2f3f27be03a93379d1ba16a1450a7b1aacfa0366e2c0dd/cffi-1.11.5-cp36-cp36m-manylinux1_x86_64.whl Collecting fast5_research (from -r conda_reqs.txt (line 6)) Collecting intervaltree (from -r conda_reqs.txt (line 7)) Collecting matplotlib (from -r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/71/07/16d781df15be30df4acfd536c479268f1208b2dfbc91e9ca5d92c9caf673/matplotlib-3.0.2-cp36-cp36m-manylinux1_x86_64.whl Collecting mappy (from -r conda_reqs.txt (line 9)) Collecting msgpack-python (from -r conda_reqs.txt (line 10)) Collecting numpy (from -r conda_reqs.txt (line 11)) Using cached https://files.pythonhosted.org/packages/ff/7f/9d804d2348471c67a7d8b5f84f9bc59fd1cefa148986f2b74552f8573555/numpy-1.15.4-cp36-cp36m-manylinux1_x86_64.whl Collecting pandas (from -r conda_reqs.txt (line 12)) Using cached 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conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/0c/78/0ae9129f12098adbcfee0c51a81dfa94cdc1853142aa4d62e63c6a355bd7/progressbar2-3.39.2-py2.py3-none-any.whl Collecting h5py (from fast5_research->-r conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl Collecting sortedcontainers<3.0,>=2.0 (from intervaltree->-r conda_reqs.txt (line 7)) Using cached https://files.pythonhosted.org/packages/13/f3/cf85f7c3a2dbd1a515d51e1f1676d971abe41bba6f4ab5443240d9a78e5b/sortedcontainers-2.1.0-py2.py3-none-any.whl Collecting python-dateutil>=2.1 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl Collecting cycler>=0.10 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl Collecting kiwisolver>=1.0.1 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/69/a7/88719d132b18300b4369fbffa741841cfd36d1e637e1990f27929945b538/kiwisolver-1.0.1-cp36-cp36m-manylinux1_x86_64.whl Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl Collecting pytz>=2011k (from pandas->-r conda_reqs.txt (line 12)) Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB) 100% |████████████████████████████████| 512kB 2.8MB/s Collecting argh>=0.24.1 (from watchdog->-r conda_reqs.txt (line 15)) Using cached https://files.pythonhosted.org/packages/06/1c/e667a7126f0b84aaa1c56844337bf0ac12445d1beb9c8a6199a7314944bf/argh-0.26.2-py2.py3-none-any.whl Collecting pathtools>=0.1.1 (from watchdog->-r conda_reqs.txt (line 15)) Collecting PyYAML>=3.10 (from watchdog->-r conda_reqs.txt (line 15)) Collecting python-utils>=2.3.0 (from progressbar2->fast5_research->-r conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/eb/a0/19119d8b7c05be49baf6c593f11c432d571b70d805f2fe94c0585e55e4c8/python_utils-2.3.0-py2.py3-none-any.whl Collecting six (from progressbar2->fast5_research->-r conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Requirement already satisfied: setuptools in /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->-r conda_reqs.txt (line 8)) (40.6.3) Installing collected packages: pyzmq, aiozmq, numpy, biopython, pycparser, cffi, six, python-utils, progressbar2, h5py, fast5-research, sortedcontainers, intervaltree, python-dateutil, cycler, kiwisolver, pyparsing, matplotlib, mappy, msgpack-python, pytz, pandas, pysam, scrappie, argh, pathtools, PyYAML, watchdog Successfully installed PyYAML-3.13 aiozmq-0.7.1 argh-0.26.2 biopython-1.73 cffi-1.11.5 cycler-0.10.0 fast5-research-1.2.8 h5py-2.9.0 intervaltree-3.0.2 kiwisolver-1.0.1 mappy-2.14 matplotlib-3.0.2 msgpack-python-0.5.6 numpy-1.15.4 pandas-0.23.4 pathtools-0.1.2 progressbar2-3.39.2 pycparser-2.19 pyparsing-2.3.0 pysam-0.15.1 python-dateutil-2.7.5 python-utils-2.3.0 pytz-2018.9 pyzmq-17.1.2 scrappie-1.4.1 six-1.12.0 sortedcontainers-2.1.0 watchdog-0.9.0 . /bcl-nas/apps/anaconda3/v2018.12//etc/profile.d/conda.sh && conda activate pomoxis && python setup.py install \ --single-version-externally-managed --record=conda_install.out running install running build running build_py running build_scripts running install_lib creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis copying build/lib/pomoxis/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis copying build/lib/pomoxis/watcher.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align copying build/lib/pomoxis/align/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align copying build/lib/pomoxis/align/bwa.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align copying build/lib/pomoxis/align/common.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align copying build/lib/pomoxis/align/minimap.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align copying build/lib/pomoxis/align/py2client.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/bio.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/catalogue_errors.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/common_errors_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/coverage_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/qscores_from_summary.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/ref_seqs_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/simulate_calls.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/stats_from_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/subsample_bam.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/summary_from_stats.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/trim_alignments.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common copying build/lib/pomoxis/common/util.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common creating /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider copying build/lib/pomoxis/provider/__init__.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider copying build/lib/pomoxis/provider/replayfast5.py -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/__init__.py to __init__.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/watcher.py to watcher.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/__init__.py to __init__.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/bwa.py to bwa.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/common.py to common.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/minimap.py to minimap.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/align/py2client.py to py2client.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/__init__.py to __init__.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/bio.py to bio.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/catalogue_errors.py to catalogue_errors.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/common_errors_from_bam.py to common_errors_from_bam.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/coverage_from_bam.py to coverage_from_bam.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/qscores_from_summary.py to qscores_from_summary.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/ref_seqs_from_bam.py to ref_seqs_from_bam.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/simulate_calls.py to simulate_calls.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/stats_from_bam.py to stats_from_bam.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/subsample_bam.py to subsample_bam.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/summary_from_stats.py to summary_from_stats.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/trim_alignments.py to trim_alignments.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/common/util.py to util.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider/__init__.py to __init__.cpython-36.pyc byte-compiling /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis/provider/replayfast5.py to replayfast5.cpython-36.pyc running install_egg_info running egg_info writing pomoxis.egg-info/PKG-INFO writing dependency_links to pomoxis.egg-info/dependency_links.txt writing entry points to pomoxis.egg-info/entry_points.txt writing requirements to pomoxis.egg-info/requires.txt writing top-level names to pomoxis.egg-info/top_level.txt reading manifest file 'pomoxis.egg-info/SOURCES.txt' writing manifest file 'pomoxis.egg-info/SOURCES.txt' Copying pomoxis.egg-info to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/lib/python3.6/site-packages/pomoxis-0.2.0-py3.6.egg-info running install_scripts copying build/scripts-3.6/assess_assembly -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin copying build/scripts-3.6/intersect_assembly_errors -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin copying build/scripts-3.6/mini_align -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin copying build/scripts-3.6/mini_assemble -> /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/assess_assembly to 755 changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/intersect_assembly_errors to 755 changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/mini_align to 755 changing mode of /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin/mini_assemble to 755 Installing align_serve script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing catalogue_errors script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing common_errors_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing coverage_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing coverage_from_fastx script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing fast_convert script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing long_fastx script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing pomoxis_path script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing qscores_from_summary script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing read_until_filter script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing ref_seqs_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing simulate_calls script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing split_fastx script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing stats_from_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing subsample_bam script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing summary_from_stats script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin Installing trim_alignments script to /bcl-nas/apps/anaconda3/v2018.12/envs/pomoxis/bin writing list of installed files to 'conda_install.out' rm conda_reqs.txt
cjw85 commented 5 years ago

I believe this is an issue with using python 3.7: a quick look at the python 3.7 release notes tells me async and await are now reserved keywords, so the above code is not valid python 3.7.

As such pomoxis is not compatible with python 3.7 (and isnt likely to be made so in the immediate future).

mjfi2sb3 commented 5 years ago

Hi @cjw85;

yes, I created a virtual environment for python 3.6 under anaconda (conda create -n py36 python=3.6 anaconda) then installed pomoxis in this environment as you described (CONDA=/bcl-nas/apps/anaconda3/v2018.12_02/envs/py36/ make conda). This seems to have solved the problem and all tools seem to work including those that call porechop.

Best & thanks again. /SB

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cjw85 commented 5 years ago

Thanks for confirming everything is now working.