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

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:

#!/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...

#!/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...

#!/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...

#!/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...

#!/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...