## Command manual Here we provide a full description of the various commands and their various options. In the command line, you can always type `motus ` to obtain a short description of the various flags and useage. To execute the motus profiler you need to call `motus [options]`. The possible values for command are: * `profile`, perform taxonomic profiling on a sample (`map_tax` + `calc_mgc` + `calc_motu`); * `merge`, append different profiles to create a table. The profile command can be split into: * `map_tax`, map reads to the marker gene database, output a SAM/BAM file; * `calc_mgc`, aggregate reads from the same marker gene cluster (mgc) and output the mgc abundance table. It uses the SAM/BAM file produced by map_tax; * `calc_motu`, from a mgc abundance table (created by calc_mgc), produce the mOTUs abundance table; We also have a command to handle long reads. You can find a more detailed tutorial [here](long_reads.md). * `prep_long`, which converts long read data into short read data, which can then be used by mOTUs profile . And commands to perform SNV profiling using the metaSNV package [https://metasnv.embl.de/](https://metasnv.embl.de/). Again you have a more detailed tutorial using these commands [here](SNV_profiling.md). * `map_snv`, map reads to the mOTUs marker gene database and produce a BAM file suitable for metaSNV. * `snv_call`, SNV calling using metaSNV ### `profile` Performs taxonomic profiling from reads in fastq format, outputs the relative abundances of each profiled species. **Input options** | Option | Input type | Description | Example | | | | |-----------|-------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----|-----|-----| | `-f` | FILE[,FILE] | Input fastq file in the forward orientation. When present, it requires also `-r` to be present. The file(s) can also be a ZIP file (.gz or .bz2). Multiple files as in the case reads of analyzed in two lanes need to be comma-separated. | `motus profile -f sample_lane1_1.fq,for_sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq > sample.motus` | | | | | `-r` | FILE[,FILE] | Input fastq file(s) in the reverse orientation. When present, it requires also `-f` to be present. The file(s) can also be a ZIP file (.gz or .bz2). Multiple files as in the case of reads analyzed in two lanes need to be comma-separated. It is important to be consistent in the order of the files | `motus profile -f sample_lane1_1.fq,for_sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq > sample.motus` | | | | | `-s` | FILE[,FILE] | Input fastq file(s) for unpaired reads, The file(s) can also be a ZIP file (.gz or .bz2). You can also analyze single read files alone or together with forward and reverse reads. | `motus profile -s sample_lane1.fq,sample_lane2.fq > sample.motus ` \motus profile -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -s sample_lane1.fq > sample.motus` | | | | | `-n` | STR | Name of the sample. Supplying a unique name is essential for merging profiles later on. | `motus profile -f sample_lane1_1.fq,for_sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -n sample > sample.motus` | | | | | `-i` | FILE | From the intermediate alignment result of `map_tax`( as produced by the `-I` option) as input, create a taxonomic profile | `motus profile -i sample.bam > sample.motus` | | | | | `-db` | DIR | Provide a different database directory DIR | If the database is in directory `~/database`
`motus profile -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -db ~/database > sample.motus` | | | | | `-m` | FILE | From the intermediate MGC read count table (as produced by the `-M` option) as input, create a taxonomic profile | `motus profile -m sample.mgc > sample.motus` | | | | **Output options** | Option | Input type | Description | Example | |-----------|---------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------| | `-o` | FILE | Output file name. If you don't provide this option then it will print to *stdout*. | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus ` | | `-I` | FILE | Save the intermediate alignment result of `map_tax` in .bam format in FILE | `motus -f sample_1.fq -r sample_2.fq -I sample.bam > sample.motus` | | `-M` | FILE | Save the intermediate marker gene cluster (MGC) read count table result from `calc_mgc` in FILE | `motus profile -f sample_1.fq -r sample_2.fq -M sample.mgc > sample.motus ` | | `-e` | | Print the abundances of only the ref-mOTUs in the output. All other mOTU types (meta and ext) will be part of `unassigned` | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -e ` | | `-c` | | Output the taxonomic profile with counts rather than relative abundances | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -c ` | | `-p` | | Print the NCBI TaxID of the mOTU in the output | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -p ` | | `-B` | | Output the taxonomy profile in BIOM format | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -B ` | | `-C` | STR | Print result in CAMI format (BioBoxes format 0.9.1). Possible values: [precision, recall, parenthesis]. Note that the mOTUs species definition and the NCBI species definition is not always congruent. As a result, you can decide three methods to save the result in CAMI format: "precision", where the discrepancies are deleted; "recall", where the relative abundances of the discrepancies are split and "parenthesis" where all the discrepancies are kept. | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -P precision ` | | `-q` | | Report the full rank taxonomy in the taxonomic profile output | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -q ` | | `-k` | STR | Report abundances at a specific taxonomic level. You can choose between [kingdom, phylum, class, order, family, genus, mOTU]. | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -k phylum ` | | `-A` | | Print all taxonomic levels together (kingdom to mOTUs; overrides `-k`) | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -A` | **Algorithm options** | Option | Input type | Description | Example | |-----------|--------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------| | `-g` | INT [Default 3] | Number of marker genes required to calculate a mOTU’s abundance. Given a mOTU, we calculate its abundance if at least `-g` marker genes have a read count different from 0. A value equal to 1 produces results with higher recall, while higher values produce results with higher precision. The minimum value is 1 and the maximum is 10. Default: 3 | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -g 1` | | `-l` | INT [Default 75] | Minimum alignment length for reads. This has to be lower than the average read length; a warning will be produced in the *stderr* if `l` is larger than the average read length. A smaller value produces higher recall while a larger value will produce higher precision. Default: 75 | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -l 60` | | `-t` | INT [Default 1] | Number of threads to use when running `bwa`. It is suggested to use multiple threads so that bwa will run faster. | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -t 4` | | `-y` | STR [Default insert.scaled_count] | Type of read counts that we use. Possible values: [base.coverage, insert.raw_counts, insert.scaled_counts] | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -y base.coverage` | | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus profile -f sample_1.fq -r sample_2.fq -o sample.motus -v 1` | ### `merge` Merges taxnonomic profiles from multiple samples into one (tab-separated) table. Requires that each profile is named (using `-n` in `motus profile`). **Input options** | Option | Input type | Description | Example | |-----------|---------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | `-i` | [,FILE] | List of profiled samples to be merged. It is important that each profile has a unique name (given by `-n` flag in `motus profile` ). | `motus merge -i sampleA.motus,sampleB.motus > merged.motus` | | `-d` | DIR | Merge all profiles within directory DIR. Note that the command will fail if any file other than mOTUs profiles are present in the directory. | If all profiles to be merged are in DIR `results/`:
`motus merge -d results > merged.motus` | | `-a` | STR [,STR] | Append profiles pre-computed using publicly available metagenomic and metatransciptomic samples from various environments (available from `mOTUs` versions 2.6 and up) to your own profilles. A total of `x` public profiles are available from the following environments: [all, air, bioreactor, bee, cat, marine, mouse, pig, sheep, soil, termite, wastewater]. You can append profiles from a single environment or multiple environments. | Appending profiles from a single environment:`motus merge -d results -a human > merged.motus`
Appending profiles from multiple environments: `motus merge -d results -a human,cat`
Appending all public profiles: `motus merge -d results -a all > merged.motus` | **Output options** | Option | Input type | Description | Example | |-----------|---------------|---------------------------------------------------------------------------------------|--------------------------------------------------------------------| | `-o` | FILE | Output file name. If you don't provide this option then it will print to *stdout*. | `motus merge -i sampleA.motus,sampleB.motus -o merged.motus` | | `-B` | | Print result in BIOM format | `motus merge -i sampleA.motus,sampleB.motus -o merged.motus -B` | **Algorithm options** | Option | Input type | Description | Example | |-----------|--------------------|------------------------------------------------------------------------|----------------------------------------------------------------------| | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus merge -i sampleA.motus,sampleB.motus -o merged.motus -v 2` | ### `map_tax` Maps reads from fastq files to marker gene database, outputs a SAM/BAM file. **Input options** | Option | Input type | Description | Example | |-----------|-------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | `-f` | FILE[,FILE] | Input fastq file in the forward orientation. When present, it requires also `-r` to be present. The file(s) can also be a ZIP file (.gz or .bz2). Multiple files as in the case reads of analyzed in two lanes need to be comma-separated. | `motus map_tax -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq > sample.sam` | | `-r` | FILE[,FILE] | Input fastq file(s) in the reverse orientation. When present, it requires also `-f` to be present. The file(s) can also be a ZIP file (.gz or .bz2). Multiple files as in the case of reads analyzed in two lanes need to be comma-separated. It is important to be consistent in the order of the files | `motus map_tax -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq > sample.sam` | | `-s` | FILE[,FILE] | Input fastq file(s) for unpaired reads, The file(s) can also be a ZIP file (.gz or .bz2). You can also analyze single read files alone or together with forward and reverse reads. | `motus map_tax -s sample_lane1.fq,sample_lane2.fq > sample.sam` `
motus map_tax -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -s sample_lane1.fq > sample.sam` | | `-db` | DIR | Provide a different database directory DIR | If the database is in directory `~/database`
`motus map_tax -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -db ~/database > sample.sam` | **Output options** | Option | Input type | Description | Example | |-----------|---------------|---------------------------------------------------------------------------------------|-------------------------------------------------| | `-o` | FILE | Output file name. If you don't provide this option then it will print to *stdout*. | `motus map_tax -s sample.fq -o sample.sam` | | `-b` | | Save the result of `bwa` in bam format | `motus map_tax -s sample.fq -b > sample.bam` | **Algorithm options** | Option | Input type | Description | Example | |-----------|---------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------| | `-t` | INT | Number of threads to use when running `bwa`. It is suggested to use multiple threads so that bwa will run faster. | `motus map_tax -f sample_1.fq -r sample_2.fq -o sample.sam -t 4` | | `-l` | INT [Default 75] | Minimum alignment length for reads. This has to be lower than the average read length; a warning will be produced in the *stderr* if `l` is larger than the average read length. A smaller value produces higher recall while a larger value will produce higher precision. Default: 75 | `motus map_tax -f sample_1.fq -r sample_2.fq -o sample.sam -l 60` | | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus map_tax -s sample.fq -o sample.sam -v 2` | ### `calc_mgc` Aggregate reads from the same marker gene cluster (mgc) and outputs the mgc abundance table. It uses the SAM/BAM file produced by `map_tax`. **Input options** | Option | Input type | Description | Example | |-----------|-----------------|-----------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------| | `-i` | FILE [,FILE] | Input SAM or BAM file (or list of files) result of `motus map_tax`. The program automatically recognizes the right extension. | `motus calc_mgc -i sample.bam > mgc_reads.count`
`motus calc_mgc -i sample1_lane1.bam,sample1_lane2.sam > mgc_reads.count ` | | `-n` | STR | Name of the sample. Supplying a unique name is essential for merging profiles later on. | `motus calc_mgc -i sample.bam -n sample > mgc_reads.count ` | | `-db` | DIR | Provide a different database directory DIR | `motus calc_mgc -i sample.bam -db ~/database > mgc_reads.count` | **Output options** | Option | Input type | Description | Example | |-----------|-----------------|-----------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------| | `-i` | FILE [,FILE] | Input SAM or BAM file (or list of files) result of `motus map_tax`. The program automatically recognizes the right extension. | `motus calc_mgc -i sample.bam > mgc_reads.count`
`motus calc_mgc -i sample1_lane1.bam,sample1_lane2.sam > mgc_reads.count ` | | `-n` | STR | Name of the sample. Supplying a unique name is essential for merging profiles later on. | `motus calc_mgc -i sample.bam -n sample > mgc_reads.count ` | | `-db` | DIR | Provide a different database directory DIR | `motus calc_mgc -i sample.bam -db ~/database > mgc_reads.count` | **Algorithm options** | Option | Input type | Description | Example | |-----------|--------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------| | `-l` | INT [Default 75] | Minimum alignment length for reads. This has to be lower than the average read length; a warning will be produced in the *stderr* if `l` is larger than the average read length. A smaller value produces higher recall while a larger value will produce higher precision. Default: 75 | `motus calc_mgc -i sample.bam -y insert.raw_counts -l 50 -o mgc_reads.count ` | | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus calc_mgc -i sample.bam -v 2 > mgc_reads.count ` | | `-y` | STR [Default insert.scaled_count] | Type of read counts that we use. Possible values: [base.coverage, insert.raw_counts, insert.scaled_counts] | `motus calc_mgc -i sample.bam -y insert.raw_counts -o mgc_reads.count ` | ### `calc_motu` Produces the mOTUs abundance table (final output of `motus profile`) from a mgc abundance table (created by `calc_mgc`). **Input options** | Option | Input type | Description | Example | |-----------|---------------|---------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | `-i` | FILE | Input MGC read count table (produced by `motus calc_mgc`) | `motus calc_motu -i mgc_reads.count > sample.motus` | | `-n` | STR | Name of the sample. Supplying a unique name is essential for merging profiles later on. | `motus calc_motu -i mgc_reads.count -n sample > sample.motus` | | `-db` | DIR | Provide a different database directory DIR | If the database is in directory `~/database`
`motus -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -db ~/database > sample.motus` | **Output options** | Option | Input type | Description | Example | |-----------|---------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------| | `-o` | FILE | Output file name. If you don't provide this option then it will print to *stdout*. | `motus calc_motu -i mgc_reads.count -o sample.motus` | | `-e` | | Print the abundances of only the ref-mOTUs in the output. All other mOTU types (meta and ext) will be part of `unassigned` | `motus calc_motu -i mgc_reads.count -o sample.motus -e` | | `-c` | | Output the taxonomic profile with counts rather than relative abundances | `motus calc_motu -i mgc_reads.count -o sample.motus -c ` | | `-p` | | Print the NCBI TaxID of the mOTU in the output | `motus calc_motu -i mgc_reads.count -o sample.motus -p ` | | `-B` | | Output the taxonomy profile in BIOM format | `motus calc_motu -i mgc_reads.count -o sample.motus -B ` | | `-C` | STR | Print result in CAMI format (BioBoxes format 0.9.1). Possible values: [precision, recall, parenthesis]. Note that the mOTUs species definition and the NCBI species definition is not always congruent. As a result, you can decide three methods to save the result in CAMI format: "precision", where the discrepancies are deleted; "recall", where the relative abundances of the discrepancies are split and "parenthesis" where all the discrepancies are kept. | `motus calc_motu -i mgc_reads.count -o sample.motus -P precision ` | | `-q` | | Report the full rank taxonomy in the taxonomic profile output | `motus calc_motu -i mgc_reads.count -o sample.motus -q ` | | `-k` | STR | Report abundances at a specific taxonomic level. You can choose between [kingdom, phylum, class, order, family, genus, mOTU]. | `motus calc_motu -i mgc_reads.count -o sample.motus -k phylum ` | **Algorithm options** | Option | Input type | Description | Example | |-----------|--------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------| | `-g` | INT [Default 3] | Number of marker genes required to calculate a mOTU’s abundance. Given a mOTU, we calculate its abundance if at least `-g` marker genes have a read count different from 0. A value equal to 1 produces results with higher recall, while higher values produce results with higher precision. The minimum value is 1 and the maximum is 10. Default: 3 | `motus calc_motu -i mgc_reads.count -g 4 -o sample.motus` | | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus calc_motu -i mgc_reads.count -v 2 > sample.motus` | | `-y` | STR [Default insert.scaled_count] | Type of read counts that we use. Possible values: [base.coverage, insert.raw_counts, insert.scaled_counts] | `motus calc_mgc -i sample.bam -y insert.raw_counts -o mgc_reads.count ` | ### `prep_long` Prepares long reads to be profiled by mOTUs. **Input Options** | Option | Input type | Description | Example | |-----------|---------------|--------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------| | `i` | FILE | Input long read file to convert into shorter reads. The file can be fasta(.gz) or fastq(.gz). | `motus prep_long -i long_reads.fasta > converted_long_reads.fasta.gz` | **Output options** | Option | Input type | Description | Example | |-------------|---------------|---------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------| | `-o` | FILE | Output file name. If you don't provide this option then it will print to *stdout*. | `motus prep_long -i long_reads.fasta -o converted_long_reads.fasta.gz` | | `-no_gz` | | Do not compress the output file. | `motus prep_long -i long_reads.fasta -o converted_long_reads.fasta.gz -no_gz` | **Algorithm options** | Option | Input type | Description | Example | |-----------|----------------------|------------------------------------------------------------------------|--------------------------------------------------------------------------------------| | `-sl` | INT [Default 300] | Splitting length for the long reads. | `motus prep_long -i long_reads.fasta -o converted_long_reads.fasta.gz -sl 250` | | `-ml` | INT [Default 50] | Minimum read length. Reads shorter than `ml` are discarded. | `motus prep_long -i long_reads.fasta -o converted_long_reads.fasta.gz -ml 60` | | `-v` | INT | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus prep_long -i long_reads.fasta -o converted_long_reads.fasta.gz -v 2` | ### `map_snv` Maps reads to the marker gene database and produces a BAM file suitable for metaSNV [https://metasnv.embl.de/](https://metasnv.embl.de/). You can find a more detailed explanation on this [page](documentation/../SNV_profiling.md) **Input options** | Option | Input type | Description | Example | |-----------|-------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------| | `-f` | FILE[,FILE] | Input fastq file in the forward orientation. When present, it requires also `-r` to be present. The file(s) can also be a ZIP file (.gz or .bz2). Multiple files as in the case reads of analyzed in two lanes need to be comma-separated. | `motus map_snv -f for_sample.fastq -r rev_sample.fastq > sample.bam` | | `-r` | FILE[,FILE] | Input fastq file(s) in the reverse orientation. When present, it requires also `-f` to be present. The file(s) can also be a ZIP file (.gz or .bz2). Multiple files as in the case of reads analyzed in two lanes need to be comma-separated. It is important to be consistent in the order of the files. | `motus map_snv -f for_sample.fastq -r rev_sample.fastq > sample.bam` | | `-s` | FILE[,FILE] | Input fastq file(s) for unpaired reads, The file(s) can also be a ZIP file (.gz or .bz2). You can also analyze single read files alone or together with forward and reverse reads. | `motus map_snv -s sample_lane1.fq,sample_lane2.fq > sample.bam` | | `-db` | DIR | Provide a different database directory DIR | `motus map_snv -f sample_lane1_1.fq,sample_lane2_1.fq -r sample_lane1_2.fq,sample_lane2_2.fq -db DIR > sample.bam` | **Output options** | Option | Input type | Description | Example | |-----------|---------------|-------------------------------------------------------------------------------------------|-------------------------------------------------| | `-o` | FILE | Output BAM file name. If you don't provide this option then it will print to *stdout*. | `motus map_snv -s sample.fq > sample.bam ` | **Algorithm options** | Option | Input type | Description | Example | |-----------|---------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------| | `-l` | INT [Default 75] | Minimum alignment length for reads. | `motus map_snv -f for_sample.fastq -r rev_sample.fastq -l 50 > sample.bam` | | `-t` | INT [Default 1] | Number of threads to use | `motus map_snv -f for_sample.fastq -r rev_sample.fastq -t 4 > sample.bam` | | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus map_snv -f for_sample.fastq -r rev_sample.fastq -v 2 > sample.bam` | ### `snv_call` Performs single nucleotide variant calling using the metaSNV package [https://metasnv.embl.de/](https://metasnv.embl.de/). **Input options** | Option | Input type | Description | Example | |-----------|---------------|-------------------------------------------------------------------|---------------------------------------| | `-d` | DIR | Call metaSNV on all BAM files in the directory DIR [Mandatory] | `motus snv_call -d DIR -o out.dir` | **Output options** | Option | Input type | Description | Example | |-----------|---------------|------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------| | `-o` | DIR | Output Directory. It will fail if output directory already exists. | `motus snv_call -d DIR -o out.dir` | | `-K` | | Save in the output directory all the files and directories produced by metaSNV. By default cov, distances, filtered, snpCaller are deleted. | `motus snv_call -d DIR -o out.dir -K` | **Algorithm options** | Option | Input type | Description | Example | |-----------|-------------------------|-------------------------------------------------------------------------------------------------------------|-----------------------------------------------| | `-fb` | FLOAT [Default 80.0] | Coverage breadth, minimal horizontal genome coverage percentage per sample per species. Sample filter. | `motus snv_call -d DIR -fb 85 -o out.dir` | | `-fd` | FLOAT [Default 5.0] | Coverage depth: minimal average vertical genome coverage per sample per species. Sample filter. | `motus snv_call -d DIR -fd 20 -o out.dir` | | `-fm` | INT [Default 2] | Minimum number of samples per species. mOTU filter. | `motus snv_call -d DIR -fm 10 -o out.dir` | | `-fp` | FLOAT [Default 0.9] | Required proportion of informative samples (coverage should be non-zero) per position. Position filter. | `motus snv_call -d DIR -fp 0.8 -o out.dir` | | `-fc` | FLOAT [Default 5.0] | Minimum coverage per position per sample per species. Position filter. | `motus snv_call -d DIR -fc 10 -o out.dir` | | `-t` | INT [Default 1] | Number of threads | `motus snv_call -d DIR -t 8 -o out.dir` | | `-v` | INT [Default 3] | Change verbosity level: 1=error, 2=warning, 3=message, 4+=debugging | `motus snv_call -d DIR -v 2 -o out.dir` |