optional arguments

-h, --help

show this help message and exit

--ifn_samples IFN_SAMPLES [IFN_SAMPLES ...]

The list of sample files (space separated).The wildcard can also be used.

--mpa_pkl MPA_PKL

The database of metaphlan3.py.

--output_dir OUTPUT_DIR

The output directory.

--ifn_markers IFN_MARKERS

The marker file in fasta format.

--nprocs_main NPROCS_MAIN

The number of processors are used for the main threads. Default 1.

--nprocs_load_samples NPROCS_LOAD_SAMPLES

The number of processors are used for loading samples. Default nprocs_main.

--nprocs_align_clean NPROCS_ALIGN_CLEAN

The number of processors are used for aligning and cleaning markers. Default nprocs_main.

--nprocs_raxml NPROCS_RAXML

The number of processors are used for running raxml. Default nprocs_main.

--bootstrap_raxml BOOTSTRAP_RAXML

The number of runs for bootstraping when building the tree. Default 0.

--ifn_ref_genomes IFN_REF_GENOMES [IFN_REF_GENOMES ...]

The reference genome file names. They are separated by spaces.

--N_in_marker N_IN_MARKER

The consensus markers with the rate of N nucleotides greater than this threshold are removed. Default 0.2.

--marker_strip_length MARKER_STRIP_LENGTH

The number of nucleotides will be deleted from each of two ends of a marker. Default 50.

--marker_in_clade MARKER_IN_CLADE

In each sample, the clades with the rate of present markers less than this threshold are removed. Default 0.8.

--sample_in_clade SAMPLE_IN_CLADE

Only clades present in at least sample_in_clade samples are kept. Default 2.

--sample_in_marker SAMPLE_IN_MARKER

If the percentage of samples that a marker present in is less than this threshold, that marker is removed. Default 0.8.

--gap_in_trailing_col GAP_IN_TRAILING_COL

If the number of the trailing nucleotide columns in aligned markers with the percentage of gaps greater than gap_in_trailing_col is less than gap_trailing_col_limit, these columns will be removed. Default 0.2.

--gap_trailing_col_limit GAP_TRAILING_COL_LIMIT

If the number of the trailing nucleotide columns in aligned markers with the percentage of gaps greater than gap_in_trailing_col is less than gap_trailing_col_limit, these columns will be removed. Default 101.

--gap_in_internal_col GAP_IN_INTERNAL_COL

The internal nucleotide columns in aligned markers with the percentage of gaps greater than gap_in_internal_col will be removed. Default 0.3.

--gap_in_sample GAP_IN_SAMPLE

The samples with full sequences from all markers and having the percentage of gaps greater than this threshold will be removed. Default 0.2.

--N_col N_COL

In aligned markers, if the percentage of nucleotide columns containing more than N_count Ns less than this threshold, these columns will be removed. Default 0.8.

--N_count N_COUNT

In aligned markers, if the percentage of nucleotide columns containing more than N_count Ns less than N_col threshold, these columns will be removed. Default 0.

--long_gap_length LONG_GAP_LENGTH

In each concatenated sequence of a sample, sequential gap positions is a gap group. A gap group with length greater than this threshold is considered as a long gap group. If the ratio between the number of unique positions in all long gap groups and the concatenated sequence length is less than long_gap_percentage, these positions will be removed from all concatenated sequences. Default 2.

--long_gap_percentage LONG_GAP_PERCENTAGE

Combining this threshold with long_gap_length to removed long gaps. Default 0.8.

--p_value P_VALUE

The p_value to reject a non-polymorphic site.Default 0.05.

--clades CLADES [CLADES ...]

The clades (space separated) for which the script will compute the marker alignments in fasta format and the phylogenetic trees. If a file name is specified, the clade list in that file where each clade name is on a line will be read.Default "automatically identify all clades".

--marker_list_fn MARKER_LIST_FN

The file name containing the list of considered markers. The other markers will be discarded. Default "None".

--print_clades_only

Only print the potential clades and stop without building any tree. This option is useful when you want to check quickly all possible clades and rerun only for some specific ones. Default "False".

--alignment_program {muscle,mafft}

The alignment program. Default "muscle".

--relaxed_parameters

Set marker_in_clade=0.5, sample_in_marker=0.5, N_in_marker=0.5, gap_in_sample=0.5. Default "False".

--relaxed_parameters2

Set marker_in_clade=0.2, sample_in_marker=0.2, N_in_marker=0.8, gap_in_sample=0.8. Default "False".

--keep_alignment_files

Keep the alignment files of all markers before cleaning step.

--keep_full_alignment_files

Keep the alignment files of all markers before truncating the starting and ending parts, and cleaning step. This is equivalent to --keep_alignment_files --marker_strip_length 0

--save_sample2fullfreq

Save sample2fullfreq to a msgpack file sample2fullfreq.msgpack.

--use_threads

Use multithreading. Default "Use multiprocessing".