.. _backbone-label:

Metaphlan
==============================

Introduction
~~~~~~~~
Metaphlan is computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.


| For more information, please check:
| Docker hub: https://hub.docker.com/r/biobakery/metaphlan/tags 
| Home page: https://github.com/biobakery/MetaPhlAn

.. note::
    Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - Cluster
    - Version(s)

  * - ANVIL
    - 3.0.9, 3.0.14, 4.0.2
  * - BELL
    - 3.0.9, 3.0.14, 4.0.2
  * - GAUTSCHI
    - 3.0.9, 3.0.14, 4.0.2
  * - NEGISHI
    - 3.0.9, 3.0.14, 4.0.2
  * - SCHOLAR
    - 3.0.9, 3.0.14, 4.0.2

Commands
~~~~~~~
- metaphlan
- add_metadata_tree.py
- aggregate_scores_in_intervals.py
- align_print_template.py
- axt_extract_ranges.py
- axt_to_fasta.py
- axt_to_lav.py
- axt_to_maf.py
- bed_bigwig_profile.py
- bed_build_windows.py
- bed_complement.py
- bed_count_by_interval.py
- bed_count_overlapping.py
- bed_coverage.py
- bed_coverage_by_interval.py
- bed_diff_basewise_summary.py
- bed_extend_to.py
- bed_intersect.py
- bed_intersect_basewise.py
- bed_merge_overlapping.py
- bed_rand_intersect.py
- bed_subtract_basewise.py
- bnMapper.py
- breadth_depth.py
- cleanup-blastdb-volumes.py
- consensus.py
- consensus_aDNA.py
- div_snp_table_chr.py
- extract_markers.py
- find_in_sorted_file.py
- gene_fourfold_sites.py
- get_scores_in_intervals.py
- int_seqs_to_char_strings.py
- interval_count_intersections.py
- interval_join.py
- lav_to_axt.py
- lav_to_maf.py
- line_select.py
- lzop_build_offset_table.py
- mMK_bitset.py
- maf_build_index.py
- maf_chop.py
- maf_chunk.py
- maf_col_counts.py
- maf_col_counts_all.py
- maf_count.py
- maf_covered_ranges.py
- maf_covered_regions.py
- maf_div_sites.py
- maf_drop_overlapping.py
- maf_extract_chrom_ranges.py
- maf_extract_ranges.py
- maf_extract_ranges_indexed.py
- maf_filter.py
- maf_filter_max_wc.py
- maf_gap_frequency.py
- maf_gc_content.py
- maf_interval_alignibility.py
- maf_limit_to_species.py
- maf_mapping_word_frequency.py
- maf_mask_cpg.py
- maf_mean_length_ungapped_piece.py
- maf_percent_columns_matching.py
- maf_percent_identity.py
- maf_print_chroms.py
- maf_print_scores.py
- maf_randomize.py
- maf_region_coverage_by_src.py
- maf_select.py
- maf_shuffle_columns.py
- maf_species_in_all_files.py
- maf_split_by_src.py
- maf_thread_for_species.py
- maf_tile.py
- maf_tile_2.py
- maf_tile_2bit.py
- maf_to_axt.py
- maf_to_concat_fasta.py
- maf_to_fasta.py
- maf_to_int_seqs.py
- maf_translate_chars.py
- maf_truncate.py
- maf_word_frequency.py
- mask_quality.py
- merge_metaphlan_tables.py
- nib_chrom_intervals_to_fasta.py
- nib_intervals_to_fasta.py
- nib_length.py
- one_field_per_line.py
- out_to_chain.py
- plot_tree_graphlan.py
- poly.py
- polymut.py
- prefix_lines.py
- pretty_table.py
- qv_to_bqv.py
- random_lines.py
- read_fastx.py
- sample2markers.py
- strain_transmission.py
- sumlabels.py
- sumtrees.py
- table_add_column.py
- table_filter.py
- tfloc_summary.py
- ucsc_gene_table_to_intervals.py
- wiggle_to_array_tree.py
- wiggle_to_binned_array.py
- wiggle_to_chr_binned_array.py
- wiggle_to_simple.py
- bowtie2-build
- bowtie2

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load metaphlan

Example job
~~~~~
.. warning::
    Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead.

To run metaphlan on our clusters:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A myallocation     # Allocation name
        #SBATCH -p wholenode        # Partition name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=metaphlan
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers metaphlan

        # Your metaphlan workflow...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p cpu         # Partition name
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=metaphlan
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers metaphlan

        # Your metaphlan workflow...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p ai          # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=metaphlan
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers metaphlan

        # Your metaphlan workflow...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p a100        # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH --mem=2G       # Memory
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=metaphlan
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers metaphlan

        # Your metaphlan workflow...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A queue     # Queue name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=metaphlan
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers metaphlan

        # Your metaphlan workflow...