Failed with several errors

[AlexGaithuma]

I downloaded the SRA from your paper and run the On-rep-seq but it failed...What could be the cause?

fastqDir="/media/bioadmin/24e12c01-7941-49f5-9647-eeebabd15082/DATA/ncbi/public/sra" reusultDir="/media/bioadmin/2E1EA9711EA9332F/Analysis/ON-rep-seq" nCores="6" cd '/media/bioadmin/2E1EA9711EA9332F/On-rep-seq' (On-rep-seq) bioadmin@bioadmin-B75M-D3V-JP[On-rep-seq] snakemake -j $nCores --use-conda --config basecalled_dir=$fastqDir results_dir=$reusultDir

The ouput:

Building DAG of jobs... Creating conda environment rules/envs/R.yaml... Downloading and installing remote packages. Environment for rules/envs/R.yaml created (location: .snakemake/conda/d88797b6) Creating conda environment rules/envs/canu.yaml... Downloading and installing remote packages. Environment for rules/envs/canu.yaml created (location: .snakemake/conda/c016cea8) Creating conda environment rules/envs/On-rep-seq.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/rules/envs/On-rep-seq.yaml: Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Pip subprocess error: Running command git clone -q https://github.com/lauramilena3/Porechop /tmp/pip-req-build-fid8p3wn ERROR: Command errored out with exit status 1: command: /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"'; file='"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-cb5baidq --python-tag cp37 cwd: /tmp/pip-req-build-fid8p3wn/ Complete output (48 lines): running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/porechop copying porechop/porechop.py -> build/lib/porechop copying porechop/nanopore_read.py -> build/lib/porechop copying porechop/adapters.py -> build/lib/porechop copying porechop/init.py -> build/lib/porechop copying porechop/adapters_orig_v0.2.2.py -> build/lib/porechop copying porechop/version.py -> build/lib/porechop copying porechop/cpp_function_wrappers.py -> build/lib/porechop copying porechop/misc.py -> build/lib/porechop Cleaning previous compilation: make clean rm -f porechop/src/adapter_align.o porechop/src/alignment.o Compiling Porechop: make -j 8 g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -Wall -Wextra -pedantic -mtune=native -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp g++: error: unrecognized command line option ‘-std=c++14’ make: *** [porechop/src/adapter_align.o] Error 1 installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/porechop.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/nanopore_read.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/adapters.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/init.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/adapters_orig_v0.2.2.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/version.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/cpp_function_wrappers.py -> build/bdist.linux-x86_64/wheel/porechop copying build/lib/porechop/misc.py -> build/bdist.linux-x86_64/wheel/porechop running install_egg_info running egg_info creating porechop.egg-info writing porechop.egg-info/PKG-INFO writing dependency_links to porechop.egg-info/dependency_links.txt writing entry points to porechop.egg-info/entry_points.txt writing top-level names to porechop.egg-info/top_level.txt writing manifest file 'porechop.egg-info/SOURCES.txt' reading manifest file 'porechop.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'porechop.egg-info/SOURCES.txt' Copying porechop.egg-info to build/bdist.linux-x86_64/wheel/porechop-0.2.3-py3.7.egg-info running install_scripts error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so'

ERROR: Failed building wheel for porechop ERROR: Command errored out with exit status 1: command: /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"'; file='"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' clean --all cwd: /tmp/pip-req-build-fid8p3wn Complete output (6 lines): usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

error: option --all not recognized

ERROR: Failed cleaning build dir for porechop ERROR: Command errored out with exit status 1: command: /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"'; file='"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-s2_lr9yn/install-record.txt --single-version-externally-managed --compile cwd: /tmp/pip-req-build-fid8p3wn/ Complete output (41 lines): running install running build running build_py Cleaning previous compilation: make clean rm -f porechop/src/adapter_align.o porechop/src/alignment.o Compiling Porechop: make -j 8 g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -Wall -Wextra -pedantic -mtune=native -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp g++: error: unrecognized command line option ‘-std=c++14’ make: *** [porechop/src/adapter_align.o] Error 1 running install_lib creating /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/porechop.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/nanopore_read.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/adapters.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/init.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/adapters_orig_v0.2.2.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/version.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/cpp_function_wrappers.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop copying build/lib/porechop/misc.py -> /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/porechop.py to porechop.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/nanopore_read.py to nanopore_read.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/adapters.py to adapters.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/init.py to init.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/adapters_orig_v0.2.2.py to adapters_orig_v0.2.2.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/version.py to version.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-37.pyc byte-compiling /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop/misc.py to misc.cpython-37.pyc running install_egg_info running egg_info writing porechop.egg-info/PKG-INFO writing dependency_links to porechop.egg-info/dependency_links.txt writing entry points to porechop.egg-info/entry_points.txt writing top-level names to porechop.egg-info/top_level.txt reading manifest file 'porechop.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'porechop.egg-info/SOURCES.txt' Copying porechop.egg-info to /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/lib/python3.7/site-packages/porechop-0.2.3-py3.7.egg-info running install_scripts Installing porechop script to /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/bin writing list of installed files to '/tmp/pip-record-s2_lr9yn/install-record.txt' error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so'

ERROR: Command errored out with exit status 1: /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"'; file='"'"'/tmp/pip-req-build-fid8p3wn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-s2_lr9yn/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

CondaEnvException: Pip failed

Ran pip subprocess with arguments: ['/media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/ce54c2c7/bin/python', '-m', 'pip', 'install', '-U', '-r', '/media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/condaenv.2b27p22o.requirements.txt'] Pip subprocess output: Collecting git+https://github.com/lauramilena3/Porechop (from -r /media/bioadmin/2E1EA9711EA9332F/On-rep-seq/.snakemake/conda/condaenv.2b27p22o.requirements.txt (line 1)) Cloning https://github.com/lauramilena3/Porechop to /tmp/pip-req-build-fid8p3wn Building wheels for collected packages: porechop Building wheel for porechop (setup.py): started Building wheel for porechop (setup.py): finished with status 'error' Running setup.py clean for porechop Failed to build porechop Installing collected packages: porechop Running setup.py install for porechop: started Running setup.py install for porechop: finished with status 'error'

[lauramilena3]

Thanks for the output Alex. I suspect you are using an older version of gcc. For installing porechop you need v4.9.1 or later. You can try using this command after activating the On-rep-seq environment: conda install -c conda-forge libgcc

[AlexGaithuma]

Thanks. Upgrading gcc worked.