im trying to run a program on unix (Metaphlan2.py), however I keep getting an er

ID: 3904247 • Letter: I

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 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

You have to give arguments as:

./metaphlan2.py --fastq

it has some optional parameters also if you need you...

example of usage optional paraments

./metaphlan2.py --multifastq -x 10

If you have any doubts, please give me comment...

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