Dear authors
“UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xee in position 2: invalid continuation byte”
occurced when i use PhyloPhlAn3 to Build the phylogeny tree.in detail is
“Traceback (most recent call last):
File “~/miniconda3/envs/Metaphlan/bin/phylophlan”, line 10, in
sys.exit(phylophlan_main())
File “~/miniconda3/envs/Metaphlan/lib/python3.7/site-packages/phylophlan/phylophlan.py”, line 3276, in phylophlan_main
verbose=args.verbose)
File ~/miniconda3/envs/Metaphlan/lib/python3.7/site-packages/phylophlan/phylophlan.py”, line 826, in init_database
for f in glob.iglob(os.path.join(folder, ‘*’))
File “/~/miniconda3/envs/Metaphlan/lib/python3.7/site-packages/phylophlan/phylophlan.py”, line 827, in
for _, seq in SimpleFastaParser(bz2.open(f, ‘rt’) if f.endswith(‘.bz2’) else open(f))])
File “~/miniconda3/envs/Metaphlan/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py”, line 47, in SimpleFastaParser
for line in handle:
File “~/miniconda3/envs/Metaphlan/lib/python3.7/codecs.py”, line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xee in position 2: invalid continuation byte"
Before run Phylophlan, I use seqret to convert my metagenome data from fastq format to fna format.
and the configuration file I used by run this command:
#phylophlan_write_config_file
-o custom_config_nt.cfg
-d n
–db_dna makeblastdb
–map_dna diamond
–msa muscle
–trim trimal
–tree1 fasttree
–tree2 raxml
can you help me to solve this problem?
Good luck for you