request for your help to install ete3
Amit Rai
Dear Sir/Mam,
My name is Amit Rai, working as research scientist from RIKEN, Japan.
I am writing here as I wanted to install and use ete3. I tried to use it through conda, but got the error below. I started with creating a new conda environment and then used this command-
conda activate ete3_latest
conda install -c etetoolkit ete3 ete_toolchain
I will appreciate any help here.
Thank you so much,
With best regards
Amit
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 132, in conda_http_errors
yield
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 101, in repodata
response.raise_for_status()
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://conda.anaconda.org/etetoolkit/linux-64/current_repodata.json
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/requests/models.py", line 971, in json
return complexjson.loads(self.text, **kwargs)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/simplejson/__init__.py", line 525, in loads
return _default_decoder.decode(s)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/simplejson/decoder.py", line 372, in decode
obj, end = self.raw_decode(s)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/simplejson/decoder.py", line 402, in raw_decode
return self.scan_once(s, idx=_w(s, idx).end())
simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1124, in __call__
return func(*args, **kwargs)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 69, in main_subshell
exit_code = do_call(args, p)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 91, in do_call
return getattr(module, func_name)(args, parser)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/notices/core.py", line 109, in wrapper
return func(*args, **kwargs)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 264, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 132, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 175, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 280, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/common/io.py", line 84, in decorated
return f(*args, **kwds)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 447, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 1060, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/index.py", line 267, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 124, in query_all
result = tuple(chain.from_iterable(executor.map(subdir_query, channel_urls)))
File "/mnt/HD1/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/mnt/HD1/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 446, in result
return self.__get_result()
File "/mnt/HD1/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/mnt/HD1/miniconda3/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 113, in <lambda>
subdir_query = lambda url: tuple(
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 129, in query
self.load()
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 215, in load
_internal_state = self._load()
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 323, in _load
raw_repodata_str = self._repo.repodata(mod_etag_headers)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 101, in repodata
response.raise_for_status()
File "/mnt/HD1/miniconda3/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 179, in conda_http_errors
raise RepodataIsEmpty(
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 461, in __init__
body = response.json()
File "/mnt/HD1/miniconda3/lib/python3.9/site-packages/requests/models.py", line 975, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
`$ /mnt/HD1/miniconda3/bin/conda install -c etetoolkit ete3 ete_toolchain`
environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_ADDR2LINE=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-addr2line
CONDA_BACKUP_AR=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-ar
CONDA_BACKUP_AS=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-as
CONDA_BACKUP_BUILD=x86_64-conda-linux-gnu
CONDA_BACKUP_CC=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-cc
CONDA_BACKUP_CC_FOR_BUILD=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-cc
CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/mnt/HD1/miniconda3/include -march=nocona -mtune=haswell -ftree-
vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-
sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_CMAKE_PREFIX_PATH=/mnt/HD1/miniconda3:/mnt/HD1/miniconda3/x86_64-conda-linux-
gnu/sysroot/usr
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/mnt/HD1/miniconda3/x86_64-conda-linux-gnu/sysroot
CONDA_BACKUP_CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
CONDA_BACKUP_CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
CONDA_BACKUP_CPP=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-cpp
CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/HD1/miniconda3/include
-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_CXX=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-c++
CONDA_BACKUP_CXXFILT=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-c++filt
CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/mnt/HD1/miniconda3/include -fvisibility-inlines-hidden -std=c++17
-fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC
-fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
-isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_CXX_FOR_BUILD=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-c++
CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /mnt/HD1/miniconda3/include
-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/mnt/HD1/miniconda3/include -fopenmp -march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall
-Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-
assignments -ffunction-sections -pipe -fopenmp -march=nocona
-mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-
plt -O2 -ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/mnt/HD1/miniconda3/include -fopenmp -march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall
-Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-
assignments -ffunction-sections -pipe -fopenmp -march=nocona
-mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-
plt -O2 -ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_ELFEDIT=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-elfedit
CONDA_BACKUP_F77=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gfortran
CONDA_BACKUP_F90=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gfortran
CONDA_BACKUP_F95=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-f95
CONDA_BACKUP_FC=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gfortran
CONDA_BACKUP_FC_FOR_BUILD=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gfortran
CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/mnt/HD1/miniconda3/include -fopenmp -march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
-ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/mnt/HD1/miniconda3/include -fopenmp -march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
-ffunction-sections -pipe -isystem /mnt/HD1/miniconda3/include
CONDA_BACKUP_GCC=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gcc
CONDA_BACKUP_GCC_AR=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gcc-ar
CONDA_BACKUP_GCC_NM=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gcc-nm
CONDA_BACKUP_GCC_RANLIB=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gcc-ranlib
CONDA_BACKUP_GFORTRAN=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gfortran
CONDA_BACKUP_GPROF=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-gprof
CONDA_BACKUP_GXX=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-g++
CONDA_BACKUP_HOST=x86_64-conda-linux-gnu
CONDA_BACKUP_LD=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-ld
CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,
--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined
-Wl,-rpath,/mnt/HD1/miniconda3/lib -Wl,-rpath-
link,/mnt/HD1/miniconda3/lib -L/mnt/HD1/miniconda3/lib -Wl,-O2 -Wl,--
sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-
dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined
-Wl,-rpath,/mnt/HD1/miniconda3/lib -Wl,-rpath-
link,/mnt/HD1/miniconda3/lib -L/mnt/HD1/miniconda3/lib
CONDA_BACKUP_LD_GOLD=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-ld.gold
CONDA_BACKUP_NM=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-nm
CONDA_BACKUP_OBJCOPY=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-objcopy
CONDA_BACKUP_OBJDUMP=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-objdump
CONDA_BACKUP_RANLIB=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-ranlib
CONDA_BACKUP_READELF=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-readelf
CONDA_BACKUP_SIZE=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-size
CONDA_BACKUP_STRINGS=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-strings
CONDA_BACKUP_STRIP=/mnt/HD1/miniconda3/bin/x86_64-conda-linux-gnu-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu
CONDA_BACKUP_host_alias=x86_64-conda-linux-gnu
CONDA_DEFAULT_ENV=ete3_latest
CONDA_EXE=/mnt/HD1/miniconda3/bin/conda
CONDA_PREFIX=/mnt/HD1/miniconda3/envs/ete3_latest
CONDA_PREFIX_1=/mnt/HD1/miniconda3
CONDA_PREFIX_2=/mnt/HD1/miniconda3/envs/ete3
CONDA_PREFIX_3=/mnt/HD1/miniconda3
CONDA_PROMPT_MODIFIER=(ete3_latest)
CONDA_PYTHON_EXE=/mnt/HD1/miniconda3/bin/python
CONDA_ROOT=/mnt/HD1/miniconda3
CONDA_SHLVL=4
CURL_CA_BUNDLE=<not set>
LD_PRELOAD=<not set>
PATH=/mnt/HD1/Uncaria_rhynchophylla/analysis4paper/DupGen/data/diamond_sear
ch:/mnt/HD2/Useful_githubs/DupGen_finder:/mnt/HD2/Useful_githubs:/mnt/
HD2/Useful_githubs/EarlGrey/scripts:/mnt/HD2/Useful_githubs/EarlGrey:/
mnt/HD2/Useful_githubs/repeat_masking/RepeatModeler-2.0.2a:/mnt/HD2/Us
eful_githubs/repeat_masking/RepeatMasker/util:/mnt/HD2/Useful_githubs/
repeat_masking/RepeatMasker:/mnt/HD2/Useful_githubs/ucscTwoBitTools:/m
nt/HD2/Useful_githubs/MCScanX:/mnt/HD2/Useful_githubs/MCScanX/downstre
am_analyses:/mnt/HD2/Useful_githubs/paml4.9j/src:/mnt/HD2/Useful_githu
bs/PCF_ver3/PlantClusterFinder-1.3.0:/mnt/HD2/Useful_githubs/ncbi-blas
t-2.13.0+/bin:/mnt/HD2/Useful_githubs/Bandage_Ubuntu_dynamic_v0_8_1:/m
nt/HD1/TGS-GapCloser/zlib-1.2.11:/mnt/HD1/sratoolkit.3.0.0-ubuntu64/bi
n:/mnt/HD1/purge_dups/KMC/bin:/mnt/HD1/last-1257/bin:/mnt/HD1/GenomicC
onsensus/bin:/mnt/HD1/hifiasm:/home/amit8riken/.local/bin:/mnt/HD1/Unc
aria_rhynchophylla/analysis4paper/DupGen/data/diamond_search:/mnt/HD2/
Useful_githubs/DupGen_finder:/mnt/HD2/Useful_githubs:/mnt/HD2/Useful_g
ithubs/EarlGrey/scripts:/mnt/HD2/Useful_githubs/EarlGrey:/mnt/HD2/Usef
ul_githubs/repeat_masking/RepeatModeler-2.0.2a:/mnt/HD2/Useful_githubs
/repeat_masking/RepeatMasker/util:/mnt/HD2/Useful_githubs/repeat_maski
ng/RepeatMasker:/mnt/HD2/Useful_githubs/ucscTwoBitTools:/mnt/HD2/Usefu
l_githubs/MCScanX:/mnt/HD2/Useful_githubs/MCScanX/downstream_analyses:
/mnt/HD2/Useful_githubs/paml4.9j/src:/mnt/HD2/Useful_githubs/PCF_ver3/
PlantClusterFinder-1.3.0:/mnt/HD2/Useful_githubs/ncbi-blast-2.13.0+/bi
n:/mnt/HD2/Useful_githubs/Bandage_Ubuntu_dynamic_v0_8_1:/mnt/HD1/TGS-G
apCloser/zlib-1.2.11:/mnt/HD1/sratoolkit.3.0.0-ubuntu64/bin:/mnt/HD1/p
urge_dups/KMC/bin:/mnt/HD1/last-1257/bin:/mnt/HD1/GenomicConsensus/bin
:/mnt/HD1/hifiasm:/mnt/HD1/miniconda3/envs/ete3_latest/bin:/mnt/HD1/mi
niconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/s
bin:/bin:/usr/games:/usr/local/games:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : ete3_latest
active env location : /mnt/HD1/miniconda3/envs/ete3_latest
shell level : 4
user config file : /home/amit8riken/.condarc
populated config files : /home/amit8riken/.condarc
conda version : 23.1.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.31=0
__linux=5.15.0=0
__unix=0=0
base environment : /mnt/HD1/miniconda3 (writable)
conda av data dir : /mnt/HD1/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/etetoolkit/linux-64
https://conda.anaconda.org/etetoolkit/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /mnt/HD1/miniconda3/pkgs
/home/amit8riken/.conda/pkgs
envs directories : /mnt/HD1/miniconda3/envs
/home/amit8riken/.conda/envs
platform : linux-64
user-agent : conda/23.1.0 requests/2.28.2 CPython/3.9.12 Linux/5.15.0-52-generic ubuntu/20.04.4 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]: n
No report sent. To permanently opt-out, use
$ conda config --set report_errors false
