metaphlan 4 beta KeyError: 't'

Microbial community profiling MetaPhlAn
1

I just ran metaphlan 4 beta (installed from github) with mpa_vJan21_CHOCOPhlAnSGB_202103 index. The alignment goes well but at the end it gives an error:

  File "/usr/local/bin/metaphlan", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/site-packages/metaphlan/metaphlan.py", line 1133, in main
    rank = ranks2code[clade.split('|')[-1][0]]
KeyError: 't'```

The command I ran:
```metaphlan --nproc 48 --input_type 'fastq' --bowtie2out metagenome.bowtie2.bz2 -o profiled_metagenome.txt --CAMI_format_output --tmp_dir /mnt/data/workdir/tmp_dir --bowtie2db /mnt/data/workdir/mpa_vJan21_CHOCOPhlAnSGB_202103 --index mpa_vJan21_CHOCOPhlAnSGB_202103 R1.fastq,R2.fastq```

The output files for the bowtie2out and for the profiled_metagenome.txt are both created. However, the profiled_metagenome.txt file container results up to species level, without the SGBs level.
2

Hi @ilyavs
MetaPhlAn 4 is a still-not-published beta version, thus some problems could be encountered during the execution with really specific parameters. In this case, the problem seems related to the use of the --CAMI_format_output parameter. Briefly, while in the CAMI output format the t__ level describes the strain level, in MetaPhlAn 4 the t__ level describes the SGB level (Redirecting) and thus. they are not comparable. This is why when executing with the --CAMI_format_output, metaphlan only produces the table up to the species level. But thanks for reporting this, we will remove the error produced (as it is the expected behaviour) in the next version.