Metaphlan 3 issue reading gzipped paired end input

[flannsmith]

Describe the bug
I updated to metaphlan 3 and am not able to run metaphlan on paired-end files. This is probably a really simple syntax error (apologies if so) but I am puzzled as to what I'm doing wrong.

I followed the structure of the command on here https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0

$ metaphlan metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt

by putting a comma and no space between the 2 files

To Reproduce
metaphlan S122_paired_1.fastq,gz,S122_paired_2.fastq.gz --bowtie2out S122.bowtie2.bz2 --input_type fastq --add_viruses --unknown_estimation -o profiled_metagenome.txt

Error I get:
Traceback (most recent call last):
File "/home/linda/.local/bin/read_fastx.py", line 8, in
sys.exit(main())
File "/home/linda/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 155, in main
nreads += read_and_write_raw(f, opened=False, min_len=min_len)
File "/home/linda/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 119, in read_and_write_raw
nreads = read_and_write_raw_int(inf, min_len=min_len)
File "/home/linda/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 64, in read_and_write_raw_int
l = fd.readline()
File "/usr/lib/python3.6/gzip.py", line 289, in read1
return self._buffer.read1(size)
File "/usr/lib/python3.6/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/lib/python3.6/gzip.py", line 463, in read
if not self._read_gzip_header():
File "/usr/lib/python3.6/gzip.py", line 411, in _read_gzip_header
raise OSError('Not a gzipped file (%r)' % magic)
OSError: Not a gzipped file (b'#S')

If try again with a space between (as in metaphlan 2 documentation)

metaphlan S122_paired_1.fastq.gz, S122_paired_2.fastq.gz --bowtie2out S122.bowtie2.bz2 --input_type fastq --add_viruses --unknown_estimation -o profiled_metagenome.txt

I get the error:

File "/home/linda/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 53, in fopen
return open(fn)
FileNotFoundError: [Errno 2] No such file or directory: ''

Platform (please complete the following information):

• MetaPhlAn version 3.0 (20 Mar 2020)
• Installed from source (cloned git repository)

What am I missing? Thanks!

[fbeghini]

metaphlan S122_paired_1.fastq,gz,S122_paired_2.fastq.gz --bowtie2out S122.bowtie2.bz2 --input_type fastq --add_viruses --unknown_estimation -o profiled_metagenome.txt

has a comma instead of a dot in the first file extension, this is the correct command

metaphlan S122_paired_1.fastq.gz,S122_paired_2.fastq.gz --bowtie2out S122.bowtie2.bz2 --input_type fastq --add_viruses --unknown_estimation -o profiled_metagenome.txt

Next time, please read note #123