HUMAnN4 alpha demo.fastq file not working

Microbial community profiling HUMAnN
1

I tried running the new HUMAnN version (4 aplha) but I keep getting an error from metaphlan

humann -i demo.fastq -o demo --input-format 'fastq'     
Output files will be written to: /mnt/omar/misc/tests/humann_test/demo

Running metaphlan ........                                                                                                                                        -o /mn
                                                                                                                                                                  lan_bo
CRITICAL ERROR: Error executing: /home/omar/Downloads/miniconda3/envs/humann_env/bin/metaphlan /mnt/omar/misc/tests/humann_test/demo.fastq -t rel_ab_w_read_stats -o /mnt/omar/misc/tests/humann_test/demo/demo_1_metaphlan_profile.tsv --input_type error --bowtie2out /mnt/omar/misc/tests/humann_test/demo/demo_humann_temp/demo_metaphlan_bowtie2.txt

Error message returned from metaphlan :
usage: metaphlan --input_type {fastq,fasta,bowtie2out,sam} [--force]
                 [--bowtie2db METAPHLAN_BOWTIE2_DB] [-x INDEX]
                 [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE]
                 [--bowtie2_build BOWTIE2_BUILD] [--bowtie2out FILE_NAME]
                 [--min_mapq_val MIN_MAPQ_VAL] [--no_map] [--tmp_dir]
                 [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len]
                 [--min_alignment_len] [--add_viruses] [--ignore_eukaryotes]
                 [--ignore_bacteria] [--ignore_archaea] [--ignore_ksgbs]
                 [--ignore_usgbs] [--stat_q] [--perc_nonzero]
                 [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat]
                 [-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS]
                 [--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab]
                 [--profile_vsc] [--vsc_out VSC_OUT]
                 [--vsc_breadth VSC_BREADTH] [-o output file]
                 [--sample_id_key name] [--use_group_representative]
                 [--sample_id value] [-s sam_output_file] [--legacy-output]
                 [--CAMI_format_output] [--unclassified_estimation] [--mpa3]
                 [--biom biom_output] [--mdelim mdelim] [--nproc N]
                 [--subsampling SUBSAMPLING]
                 [--subsampling_output SUBSAMPLING_OUTPUT]
                 [--subsampling_paired SUBSAMPLING_PAIRED] [-1 FORWARD_READS]
                 [-2 REVERSE_READS] [--mapping_subsampling]
                 [--subsampling_seed SUBSAMPLING_SEED] [--install] [--offline]
                 [--force_download] [--read_min_len READ_MIN_LEN] [-v] [-h]
                 [INPUT_FILE] [OUTPUT_FILE]
metaphlan: error: argument --input_type: invalid choice: 'error' (choose from 'fastq', 'fasta', 'bowtie2out', 'sam')

P.S. It doesn’t work even when I remove the --input-format flag

2

Getting caught up here. Were you able to resolve this? It’s not obvious to me from the error message what is going wrong. The first thing I would try is running MetaPhlAn on our sample outside of HUMAnN to see if that works (if not, there might be something wrong with the MetaPhlAn install itself).