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moldach/fastqc_wrapper_nohup.out

Created September 22, 2020 23:01
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Error log from snakemake fastqc wrapper when using --use-singularity and --use-conda on HPC
Raw
fastqc_wrapper_nohup.out
Workflow defines that rule get_vep_cache is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
Creating conda environment https:/github.com/snakemake/snakemake-wrappers/raw/0.66.0/bio/vep/plugins/environment.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /tmp/tmpisqd78u6.yaml:
Solving environment: ...working... failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/conda/exceptions.py", line 819, in __call__
return func(*args, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/conda_env/cli/main.py", line 74, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/opt/conda/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 108, in execute
installer.install(prefix, pkg_specs, args, env)
File "/opt/conda/lib/python3.7/site-packages/conda_env/installers/conda.py", line 35, in install
unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))
File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 518, in solve_for_transaction
force_remove, force_reinstall)
File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 451, in solve_for_diff
final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 180, in solve_final_state
index, r = self._prepare(prepared_specs)
File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 592, in _prepare
self.subdirs, prepared_specs)
File "/opt/conda/lib/python3.7/site-packages/conda/core/index.py", line 215, in get_reduced_index
new_records = query_all(spec)
File "/opt/conda/lib/python3.7/site-packages/conda/core/index.py", line 184, in query_all
return tuple(concat(future.result() for future in as_completed(futures)))
File "/opt/conda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 95, in query
self.load()
File "/opt/conda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 149, in load
_internal_state = self._load()
File "/opt/conda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 227, in _load
mod_etag_headers.get('_mod'))
File "/opt/conda/lib/python3.7/site-packages/conda/core/subdir_data.py", line 437, in fetch_repodata_remote_request
timeout=timeout)
File "/opt/conda/lib/python3.7/site-packages/requests/sessions.py", line 525, in get
return self.request('GET', url, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/requests/sessions.py", line 512, in request
resp = self.send(prep, **send_kwargs)
File "/opt/conda/lib/python3.7/site-packages/requests/sessions.py", line 622, in send
r = adapter.send(request, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/requests/adapters.py", line 412, in send
self.cert_verify(conn, request.url, verify, cert)
File "/opt/conda/lib/python3.7/site-packages/requests/adapters.py", line 227, in cert_verify
"invalid path: {0}".format(cert_loc))
OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/pki/tls/certs/ca-bundle.crt
`$ /opt/conda/bin/conda-env create --file /scratch/moldach/DEBUG/.snakemake/conda/9722d5b9.yaml --prefix /scratch/moldach/DEBUG/.snakemake/conda/9722d5b9`
environment variables:
ACLOCAL_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/share/aclocal
CIO_TEST=<not set>
CMAKE_LIBRARY_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/lib64
CMAKE_PREFIX_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0
CONDA_AUTO_UPDATE_CONDA=false
CONDA_EXE=/home/moldach/miniconda3/bin/conda
CONDA_PKGS_DIRS=/tmp/conda/a638ee22-5ace-407d-b4a9-54cda8ca5b4c
CONDA_PYTHON_EXE=/home/moldach/miniconda3/bin/python
CONDA_ROOT=/opt/conda
CONDA_SHLVL=0
CPATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
el2016.4/openmpi/2.1.1/include:/cvmfs/restricted.computecanada.ca/easy
build/software/2017/Core/ifort/2016.4.258/include:/cvmfs/restricted.co
mputecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/includ
e/fftw:/cvmfs/restricted.computecanada.ca/easybuild/software/2017/Core
/imkl/11.3.4.258/mkl/include
CPLUS_INCLUDE_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/include
C_INCLUDE_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/include
EASYBUILD_BUILDPATH=/tmp/moldach
LD_LIBRARY_PATH=/opt/software/slurm/lib:/.singularity.d/libs
LIBRARY_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
el2016.4/openmpi/2.1.1/lib:/cvmfs/soft.computecanada.ca/easybuild/soft
ware/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/lin
ux/compiler/lib/intel64:/cvmfs/restricted.computecanada.ca/easybuild/s
oftware/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/
linux/compiler/lib/intel64:/cvmfs/soft.computecanada.ca/easybuild/soft
ware/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linux
/compiler/lib/intel64:/cvmfs/restricted.computecanada.ca/easybuild/sof
tware/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linu
x/compiler/lib/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profil
es/gcc-5.4.0/lib64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/g
cc-5.4.0/lib:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core
/imkl/11.3.4.258/mkl/lib/intel64:/cvmfs/restricted.computecanada.ca/ea
sybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64:/cvmfs/rest
ricted.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/l
ib/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib
LMOD_PACKAGE_PATH=/cvmfs/soft.computecanada.ca/config/lmod/
MANPATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
el2016.4/openmpi/2.1.1/share/man:/cvmfs/restricted.computecanada.ca/ea
sybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries_20
16.4.258/linux/man/common:/cvmfs/restricted.computecanada.ca/easybuild
/software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/
linux/man/common:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc
-5.4.0/share/man:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.
09/share/man:/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/sh
are/man::/opt/puppetlabs/puppet/share/man
MIC_LD_LIBRARY_PATH=/cvmfs/restricted.computecanada.ca/easybuild/software/2017/Core/imkl/1
1.3.4.258/mkl/lib/mic:/cvmfs/restricted.computecanada.ca/easybuild/sof
tware/2017/Core/imkl/11.3.4.258/lib/intel64_lin_mic
MODULEPATH=/opt/software/modulefiles:/cvmfs/soft.computecanada.ca/easybuild/modul
es/2017/avx2/MPI/intel2016.4/openmpi2.1:/cvmfs/soft.computecanada.ca/e
asybuild/modules/2017/avx2/Compiler/intel2016.4:/home/moldach/.local/e
asybuild/modules/2017/Core:/cvmfs/soft.computecanada.ca/easybuild/modu
les/2017/Core:/cvmfs/soft.computecanada.ca/custom/modules
PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin
:/bin
PKG_CONFIG_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
el2016.4/openmpi/2.1.1/lib/pkgconfig:/cvmfs/soft.computecanada.ca/nix/
var/nix/profiles/16.09/lib/pkgconfig:/cvmfs/soft.computecanada.ca/nix/
var/nix/profiles/16.09/share/pkgconfig
PYTHONPATH=/cvmfs/soft.computecanada.ca/custom/python/site-packages
REQUESTS_CA_BUNDLE=<not set>
RSNT_LD_LIBRARY_PATH=/opt/software/slurm/lib
SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt
USER_PATH=/home/moldach/snakemake-5.18.1/bin:/home/moldach/nb_distribution/:/hom
e/moldach/miniconda3/condabin:/home/moldach/projects/def-mtgraovac/mol
dach/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Com
piler/intel2016.4/openmpi/2.1.1/bin:/cvmfs/restricted.computecanada.ca
/easybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries
_2016.4.258/linux/bin/intel64:/cvmfs/restricted.computecanada.ca/easyb
uild/software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.
258/linux/bin/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profile
s/gcc-5.4.0/bin:/cvmfs/restricted.computecanada.ca/easybuild/software/
2017/Core/imkl/11.3.4.258/mkl/bin:/cvmfs/restricted.computecanada.ca/e
asybuild/software/2017/Core/imkl/11.3.4.258/bin:/cvmfs/soft.computecan
ada.ca/custom/bin/computecanada:/cvmfs/soft.computecanada.ca/easybuild
/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada
.ca/nix/var/nix/profiles/16.09/bin:/cvmfs/soft.computecanada.ca/nix/va
r/nix/profiles/16.09/sbin:/opt/software/bin:/opt/software/slurm/bin:/u
sr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/b
in:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin
__LMOD_Priority_MODULEPATH=/opt/software/modulefiles:-10
__LMOD_REF_COUNT_MODULEPATH=/opt/software/modulefiles:1;/cvmfs/soft.computecanada.ca/easybuild/mod
ules/2017/avx2/MPI/intel2016.4/openmpi2.1:1;/cvmfs/soft.computecanada.
ca/easybuild/modules/2017/avx2/Compiler/intel2016.4:1;/home/moldach/.l
ocal/easybuild/modules/2017/Core:1;/cvmfs/soft.computecanada.ca/easybu
ild/modules/2017/Core:1;/cvmfs/soft.computecanada.ca/custom/modules:1
active environment : None
shell level : 0
user config file : /scratch/moldach/DEBUG/.condarc
populated config files :
conda version : 4.5.11
conda-build version : not installed
python version : 3.7.0.final.0
base environment : /opt/conda (read only)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/linux-64
https://repo.anaconda.com/pkgs/pro/noarch
package cache : /tmp/conda/a638ee22-5ace-407d-b4a9-54cda8ca5b4c
envs directories : /scratch/moldach/DEBUG/.conda/envs
/opt/conda/envs
platform : linux-64
user-agent : conda/4.5.11 requests/2.19.1 CPython/3.7.0 Linux/3.10.0-1062.12.1.el7.x86_64 debian/9 glibc/2.24
UID:GID : 3019658:3019658
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
File "/home/moldach/snakemake-5.18.1/lib/python3.7/site-packages/snakemake/deployment/conda.py", line 335, in create
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