Error when checking dependencies in mdmcleaner makedb

[danpal96]

Installation with conda:
python=3.11.3
mdmcleaner=0.8.7

I got the next error when running mdmcleaner makedb

You are running the following MDMcleaner command:                                                                                
         '/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/bin/mdmcleaner makedb -o mdmcleaner'                                                                                                                                                             
reading settings from configfile: "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/mdmcleaner.config"                                                                                                              
                                                                                                                                                                                                                                                                  
        settings:                                                                                                                                                                                                                                                 
                threads = '1'                                                                                                                                                                                                                                     
                db_type = '['gtdb']'                                                                                                                                                                                                                              
                blacklistfile = '['/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/blacklist.list']'                                                                                                               
                blastn = 'blastn'                                                                                                
                blastp = 'blastp'                                                                                                
                makeblastdb = 'makeblastdb'                                                                                                                                                                                                                       
                blastdbcmd = 'blastdbcmd'                                                                                                                                                                                                                         
                diamond = 'diamond'                                                                                                                                                                                                                               
                barrnap = 'barrnap'                                                                                              
                hmmsearch = 'hmmsearch'                                                                                          
                aragorn = 'aragorn'                                                                                              
                prodigal = 'prodigal'                                                                                                                                                                                                                             
                                                                                                                                 
                                                                                                                                 
        checking dependencies...                                                                                                 
                makeblastdb...2.13.0 --> OK!                                                                                     
                diamond...2.1.6 --> OK!                                                                                                                                                                                                                           
                wget...Traceback (most recent call last):                                                                        
  File "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/bin/mdmcleaner", line 10, in <module>                                                                                                                                                              
    sys.exit(main())                                                                                                             
             ^^^^^^                                                                                                                                                                                                                                               
  File "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/mdmcleaner.py", line 230, in main
    check_dependencies.check_dependencies("makeblastdb", "diamond", "wget", configs=configs)                                     
  File "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/check_dependencies.py", line 115, in check_dependencies                                                                                                    
    check_external_dependency(*toolnames, configs=configs)                                                                       
  File "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/check_dependencies.py", line 128, in check_external_dependency                                                                                             
    isttool = version_object(get_external_dependency_version_string(tool))                                                       
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                                                                                                         
  File "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/check_dependencies.py", line 86, in get_external_dependency_version_string
    output = proc.stdout.readline().strip()                                                                                      
             ^^^^^^^^^^^^^^^^^^^^^^                                                                                                                                                                                                                               
  File "/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/lib/python3.11/encodings/ascii.py", line 26, in decode            
    return codecs.ascii_decode(input, self.errors)[0]

For some reason it is decoding the wget --version text as ascii but in my version of wget the text contains some non-ascii characters.

I solved this by replacing the next line of get_external_dependency_version_string:

proc = subprocess.Popen(cmd, stdout = subprocess.PIPE, stderr = subprocess.STDOUT, text = True, universal_newlines=True)

with:

proc = subprocess.Popen(cmd, stdout = subprocess.PIPE, stderr = subprocess.STDOUT, text = True, universal_newlines=True, errors="ignore")

The errors parameter is explained here https://docs.python.org/3/library/io.html#io.TextIOWrapper. I don't think that setting it to ignore would cause any unexpected behaviour but I'm not sure.

[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

Copyright © 2015 Free Software Foundation, Inc.
Licence GPLv3+ : GNU GPL version 3 ou ultérieure
http://www.gnu.org/licenses/gpl.html.
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Écrit initialement par Hrvoje Nikšić hniksic@xemacs.org.
Veuillez signaler toutes anomalies ou demandes à bug-wget@gnu.org.