Options

extract

To show all available options and their default values you can type in your terminal:

captus_assembly extract --help

Input

-a, --captus_assemblies_dir

Path to the output directory from the assemble command, (e.g. 02_assemblies if you used the default name). If you didn’t assemble any sample in Captus this directory will be created in order to import your contigs assembled elsewhere.

This argument is required , the default is ./02_assemblies/

-f, --fastas

With this option you can provide the location of your own FASTA assembly files, there are several ways to list them:

  • Directory: the path to the directory containing your FASTA files assembled elsewhere. This will be the typical way to tell Captus which assemblies to import prior to marker extraction. All subdirectories will be searched for FASTA (.fa, .fna, .fasta, .fa.gz, .fna.gz, .fasta.gz) files in this case.

  • List of files: you can also provide the individual path to each of your FASTA file separated by a single space. This is useful if you only want to analyze only a couple of samples within a directory with many other samples. Another use for lists is when your FASTA assembly files are located in different directories.

  • UNIX pattern: another easy way to provide lists of files is using the wildcards * and ? to match many or just one character respectively.

Remember, all the FASTA files provided with this option will be imported to the path set by --captus_assemblies_dir

This argument is optional and has no default.

Output

-o, --out

With this option you can redirect the output directory to a path of your choice, that path will be created if it doesn’t already exist.

Inside this directory, the extracted markers for each sample will be stored in a subdirectory with the ending __captus-ext.

This argument is optinal, the default is ./03_extractions/

--max_paralogs

Maximum number of secondary hits (copies) of any particular reference marker allowed in the output. We recommend disabling the removal of paralogs (secondary hits/copies) during the extract step because the align step uses a more sophisticated filter for paralogs. This can be useful for exploratory runs, for example: if after an initial run allowing all paralogs we found out that the average number of secondary hits across samples is 5, we could use this number to get rid of outliers.

This argument is optional, the default is -1 (include all paralogs in the output).

--max_loci_files

When the number of loci in the reference exceeds this value, Captus will not write a separate FASTA file per sample per marker, otherwise the hard drive fills up with tons of small files. The file that includes all the extracted markers grouped per sample is still written (this is the only file needed by the final step align to produce the marker alignments across all samples).

This argument is optional, the default is 0 (do not write separate loci files).

--keep_all

Many intermediate files are created during the marker extraction, some are large (like BLAT’s .psl files) while others small temporary logs of intermediate steps, Captus deletes all the unnecesary intermediate files unless you enable this flag.

--overwrite

Use this flag with caution, this will replace any previous result within the output directory (for the sample names that match).

Proteins extraction global options (Scipio)

--max_loci_scipio_x2

When the number of loci in a protein reference file exceeds this number, Captus will not run a second, more exhaustive round of Scipio. Usually the results from the first round are extremely similar and sufficient, the second round can become extremely slow as the number of reference proteins grows.

This argument is optional, the default is 2000.

--predict

Scipio flags introns as dubious when the splice signals are not found at the exon edges, this may indicate that there are additional aminoacids in the recovered protein that are not present in the reference protein. Enable this flag to attempt translation of these dubious introns, if the translation does not introduce premature stop codons they will be added to the recovered protein. Recommended if you are extracting from RNA assemblies (introns would have been removed in this type of data).

Nuclear proteins (Scipio)

-n, --nuc_refs

The reference set of nuclear proteins to search and extract from the assemblies. Captus includes two sets:

  • Angiosperms353 = extract the original Angiosperms353.
  • Mega353 = extract the later expanded version of Angiosperms353; because Mega353 includes many more sequences, processing times become longer.
  • Alternatively, you can provide the path to a FASTA file (e.g. -n my_refs/my_nuclear_prots.fa) that includes your own coding references either in nucleotide or aminoacid.

If you provide a nucleotide file, please also specify the translation table to be used, otherwise Captus will translate it using --nuc_transtable 1, the “Standard code”. See the complete list of translation tables.

This argument is optional and has no default.

--nuc_transtable

If you provide a nucleotide file for extraction you can specify the genetic code to translate it.

This argument is optional, the default is 1 (= the “Standard code”. See the complete list of translation tables).

--nuc_min_score

Keep hits to the reference proteins that have at least this Scipio score. The default has been optimized to perform cross-species extraction in fragmented assemblies like the ones obtained from hybridization capture data. Accepted values are decimals from 0 to 1. For more details, read Scipio’s settings.

This argument is optional, the default is 0.13.

--nuc_min_identity

Minimum percentage of identity to the reference protein for a hit to be retained. Accepted values are any number between 0 and 100. For more details, read Scipio’s settings.

This argument is optional, the default is 65.

--nuc_min_coverage

Minimum percentage of coverage of the reference protein for a hit to be retained. Accepted values are any number between 0 and 100. For more details, read Scipio’s settings.

This argument is optional, the default is 20.

Plastidial proteins (Scipio)

-p, --ptd_refs

The reference set of plastidial proteins to search and extract from the assemblies. The options available are:

  • SeedPlantsPTD = Set of chloroplast proteins that spans all Seed Plants (curated by us).
  • Alternatively, you can provide the path to a FASTA file (e.g. -p my_refs/my_plastome_prots.fa) that includes your own coding references either in nucleotide or aminoacid.

If you provide a nucleotide file, please also specify the translation table to be used, otherwise Captus will translate it using --ptd_transtable 11, the “Bacterial, Archaeal and Plant Plastid code”. See the complete list of translation tables.

This argument is optional and has no default.

--ptd_transtable

If you provide a nucleotide file for extraction you can specify the genetic code to translate it.

This argument is optional, the default is 11 (= the “Bacterial, Archaeal and Plant Plastid code”. See the complete list of translation tables).

--ptd_min_score

Keep hits to the reference proteins that have at least this Scipio score. The default has been optimized to perform cross-species extraction in fragmented assemblies like the ones obtained from hybridization capture data. Accepted values are decimals from 0 to 1. For more details, read Scipio’s settings.

This argument is optional, the default is 0.2.

--ptd_min_identity

Minimum percentage of identity to the reference protein for a hit to be retained. Accepted values are any number between 0 and 100. For more details, read Scipio’s settings.

This argument is optional, the default is 65.

--ptd_min_coverage

Minimum percentage of coverage of the reference protein for a hit to be retained. Accepted values are any number between 0 and 100. For more details, read Scipio’s settings.

This argument is optional, the default is 20.

Mitochondrial proteins (Scipio)

-m, --mit_refs

The reference set of mitochondrial proteins to search and extract from the assemblies. The options available are:

  • SeedPlantsMIT = Set of mitochondrial proteins that spans all Seed Plants (curated by us).
  • Alternatively, you can provide the path to a FASTA file (e.g. -p my_refs/my_mitome_prots.fa) that includes your own coding references either in nucleotide or aminoacid.

If you provide a nucleotide file, please also specify the translation table to be used, otherwise Captus will translate it using --mit_transtable 1, the “Standard code” which is the genetic code used by plant mitochondria. See the complete list of translation tables.

This argument is optional and has no default.

--mit_transtable

If you provide a nucleotide file for extraction you can specify the genetic code to translate it.

This argument is optional, the default is 1 (= the “Standard code”. See the complete list of translation tables).

--mit_min_score

Keep hits to the reference proteins that have at least this Scipio score. The default has been optimized to perform cross-species extraction in fragmented assemblies like the ones obtained from hybridization capture data. Accepted values are decimals from 0 to 1. For more details, read Scipio’s settings.

This argument is optional, the default is 0.2.

--mit_min_identity

Minimum percentage of identity to the reference protein for a hit to be retained. Accepted values are any number between 0 and 100. For more details, read Scipio’s settings.

This argument is optional, the default is 65.

--mit_min_coverage

Minimum percentage of coverage of the reference protein for a hit to be retained. Accepted values are any number between 0 and 100. For more details, read Scipio’s settings.

This argument is optional, the default is 20.

Miscellaneous DNA markers (BLAT)

-d, --dna_refs

Path to a FASTA nucleotide file of miscellaneous DNA references. You can include non-coding regions, complete genes (exons + introns), complete mRNAS (including UTRs), etc.

This argument is optional and has no default.

--dna_min_identity

Minimum percentage of identity to the reference sequence for a hit to be retained. Accepted values are any number between 0 and 100.

This argument is optional, the default is 80.

--dna_min_coverage

Minimum percetange of coverage of the reference sequence for a hit to be retained. Accepted values are any number between 0 and 100.

This argument is optional, the default is 20.

Assemblies clustering (MMSeqs2)

Most contigs in your assemblies will not contain hits to your references, that means that many potentially useful markers usually remain unused and unexplored. With this feature you can cluster your unused contigs across samples to find new markers that can complement your phylogenomic dataset.

-c, --cluster_leftovers

Enable MMseqs2 clustering across samples for the contigs that had no hits to the reference markers. A new miscellaneous DNA reference is built from the best representative of each cluster in order to perform a miscellaneous DNA marker extraction.

--mmseqs_method

Select MMseqs2’s clustering algorithm. Valid options are:

  • easy-linclust = Fast linear time (for huge datasets), less sensitive clustering
  • easy-cluster = Sensitive homology search (slower)

This argument is optional, the default is easy-linclust.

--cl_mode

Select MMseqs2’s clustering mode. Valid options are:

  • 0 = Greedy set cover
  • 1 = Connected component
  • 2 = Greedy incremental (analogous to CD-HIT)

This argument is optional, the default is 2.

--cl_sensitivity

MMseqs2 sensitivity, from 1 to 7.5, only applicable when using ’easy-cluster’. Common reference points are: 1 (faster), 4 (fast), 7.5 (sens).

This argument is optional, the default is 7.5.

--cl_min_identity

Minimum percentage of similarity between sequences within a cluster. Accepted values are any number between 75 and 100. Since Captus will perform a Miscellaneous DNA marker extraction using as reference the best representative of each cluster, it is convenient to set --cl_min_identity a little lower than --dna_min_identity.

This identity threshold only affects the clustering used for the creation of the new reference of DNA markers, the actual marker extraction still depends of dna_min_identity.

This argument is optional, the default is auto (= 99% of dna_min_identity).

--cl_seq_id_mode

Select MMseqs2’s sequence identity mode. Valid options are:

  • 0 = Alignment length
  • 1 = Shorter sequence
  • 2 = Longer sequence

This argument is optional, the default is 1.

--cl_min_coverage

For a sequence to be included in a cluster, this percentage of its length has to be matched by the longest sequence in the cluster. Accepted values are number between 0 and 100.

This only affects the clustering used for the creation of the new reference of DNA markers, the actual marker extraction still depends of dna_min_coverage.

This argument is optional, the default is 80.

--cl_cov_mode

Select MMseqs2’s sequence coverage mode. Valid options are:

  • 0 = Bidirectional (query and target)
  • 1 = Target
  • 2 = Query
  • 3 = Target-in-query

This argument is optional, the default is 1.

--cl_max_seq_len

Do not cluster sequences longer than this length in bp, the maximum allowed by MMseqs2 is 65535. Use the value 0 to disable this filter.

This argument is optional, the default is 20000.

--cl_rep_min_len

After clustering is finished, only accept cluster representatives of at least this length to be part of the new miscellaneous DNA reference. This avoids the creation of very short locus alignments. Use the value 0 to disable this filter.

This argument is optional, the default is 500.

--cl_min_samples

Minimum number of samples per cluster.

This argument is optional, the default is auto (= 30% of the total number of samples or at least 4).

--cl_max_copies

Maximum average number of sequences per sample in a cluster. Helpful for excluding excessively paralogous loci.

This argument is optional, the default is 5.

--cl_tmp_dir

Path where to create the temporary directory for MMseqs2. Clustering can become slow when done on external drives, set this location to an internal drive.

This argument is optional, the default is $HOME.

Other

--scipio_path, --blat_path

If you have installed your own copies of Scipio, BLAT you can provide the full path to those copies.

These arguments are optional, the default is to use the bundled copies of these programs.

--mmseqs_path, --mafft_path

If you have installed your own copy of MMSeqs2 or MAFFT you can provide the full path to that copy.

This argument is optional, the default is mmseqs and mafft respectively.

--ram, --threads, --concurrent, --debug, --show_less

See Parallelization (and other common options)

Created by Edgardo M. Ortiz (06.08.2021)
Last modified by Edgardo M. Ortiz (14.02.2024)