Question
im trying to run a program on unix (Metaphlan2.py), however I keep getting an error reading Error: argument --input_type is required any help?? also here
im trying to run a program on unix (Metaphlan2.py), however I keep getting an error reading "Error: argument --input_type is required" any help??
also here is the script: (my PS1 is set to >>)
>> ./metaphlan2.py --input_type.fastq
Warning! Biom python library not detected!
Exporting to biom format will not work!
usage: metaphlan2.py --input_type
{fastq,fasta,multifasta,multifastq,bowtie2out,sam}
[--mpa_pkl MPA_PKL] [--bowtie2db METAPHLAN_BOWTIE2_DB]
[-x INDEX] [--bt2_ps BowTie2 presets]
[--bowtie2_exe BOWTIE2_EXE]
[--bowtie2_build BOWTIE2_BUILD] [--bowtie2out FILE_NAME]
[--no_map] [--tmp_dir] [--tax_lev TAXONOMIC_LEVEL]
[--min_cu_len] [--min_alignment_len] [--ignore_viruses]
[--ignore_eukaryotes] [--ignore_bacteria]
[--ignore_archaea] [--stat_q]
[--ignore_markers IGNORE_MARKERS] [--avoid_disqm]
[--stat] [-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS]
[--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab]
[-o output file] [--sample_id_key name]
[--sample_id value] [-s sam_output_file]
[--biom biom_output] [--mdelim mdelim] [--nproc N]
[--install] [--read_min_len READ_MIN_LEN] [-v] [-h]
[INPUT_FILE] [OUTPUT_FILE]
metaphlan2.py: error: argument --input_type is required
>>
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