Error when checking dependencies in mdmcleaner makedb

[kit-ibg-5]

Error when checking dependencies in mdmcleaner makedb

[ysevel]

got exactelly the same problem.
but I can't solve it with the same line modification:

checking dependencies...
makeblastdb...2.14.0 --> OK!
diamond...2.1.8 --> OK!
wget...None -->WARNING: Incorrect version or excecutable not detected: wget

ERROR: Not all required dependencies for running MDMcleaner are met

either wget is not detected with the modified script or I get the same error regarding ascii character if I don't:

File "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/bin/mdmcleaner", line 10, in
sys.exit(main())
File "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib/python3.7/site-packages/mdmcleaner/mdmcleaner.py", line 230, in main
check_dependencies.check_dependencies("makeblastdb", "diamond", "wget", configs=configs)
File "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib/python3.7/site-packages/mdmcleaner/check_dependencies.py", line 115, in check_dependencies
check_external_dependency(*toolnames, configs=configs)
File "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib/python3.7/site-packages/mdmcleaner/check_dependencies.py", line 128, in check_external_dependency
isttool = version_object(get_external_dependency_version_string(tool))
File "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib/python3.7/site-packages/mdmcleaner/check_dependencies.py", line 86, in get_external_dependency_version_string
output = proc.stdout.readline().strip()
File "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib/python3.7/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc2 in position 8: ordinal not in range(128)

[jvollme]

@ysevel: could you post the output of the following commands:

• which wget
• wget --version

So I can see exactly how the version string is formatted?

[ysevel]

which wget give "/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/bin/wget"

and wget --version gives: (and I think this is the problem...)

NU Wget 1.20.3 compilé sur linux-gnu.

-cares +digest -gpgme +https +ipv6 +iri +large-file -metalink +nls
+ntlm +opie -psl +ssl/openssl

Wgetrc :
/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/etc/wgetrc (système)
Paramètres régionaux :
/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/share/locale
Compilation :
/home/conda/feedstock_root/build_artifacts/wget_1632718669889/_build_env/bin/x86_64-conda-linux-gnu-cc
-DHAVE_CONFIG_H
-DSYSTEM_WGETRC="/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/etc/wgetrc"
-DLOCALEDIR="/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/share/locale"
-I. -I../lib -I../lib -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem
/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-I/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-I/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-DHAVE_LIBSSL
-I/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-DNDEBUG -march=nocona -mtune=haswell -ftree-vectorize -fPIC
-fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
-isystem
/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/wget_1632718669889/work=/usr/local/src/conda/wget-1.20.3
-fdebug-prefix-map=/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner=/usr/local/src/conda-prefix
Lien :
/home/conda/feedstock_root/build_artifacts/wget_1632718669889/_build_env/bin/x86_64-conda-linux-gnu-cc
-I/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-DHAVE_LIBSSL
-I/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-DNDEBUG -march=nocona -mtune=haswell -ftree-vectorize -fPIC
-fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
-isystem
/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/include
-fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/wget_1632718669889/work=/usr/local/src/conda/wget-1.20.3
-fdebug-prefix-map=/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner=/usr/local/src/conda-prefix
-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now
-Wl,--disable-new-dtags -Wl,--gc-sections
-Wl,-rpath,/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib
-Wl,-rpath-link,/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib
-L/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib
-lidn2
-L/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib
-lssl -lcrypto
-L/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib
-lz ftp-opie.o openssl.o http-ntlm.o ../lib/libgnu.a -lrt -lcrypto
/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib/libunistring.so
-Wl,-rpath
-Wl,/home/genouest/cnrs_umr6553/ysevellec/.conda/envs/mdmcleaner/lib

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