Command line options

To get a quick overview of all available command line options, run

nextflow run maxemil/PhyloMagnet --help

Query options

Fastq input (--fastq)

Provide one or several short read samples (with wildcards in double quotes) in fastq format to PhyloMagnet. The files can be in gzip compressed form. E.g. "fastq/*.fastq.gz".

BioProject list (--project_list)

Provide a list of BioProject identifiers (e.g. PRJNA324704) in a single file, one ID per line.

BioProject run IDs (--is_runs)

Boolean value that modifies the --project_list option such that it expects run IDs instead of Project IDs (e.g. SRR3656745). Default is false

Database (--database)

Choose if you would like to download the sra data from ncbi’s (ncbi) or ena’s (ena) servers (depending on where you are, this might make a huge speed difference). Default is ena

Reference options

EggNOG reference Ids (--reference_classes)

A file with identifiers from the EggNOG database, e.g. COG0051 or ENOG410XPEN. One ID per line.

Archived reference packages (--reference_packages)

A single path to one or several compressed references packages (see the utility script in the utils folder) from a previous PhyloMagnet run. Can contain wildcards if put in double quotes. e.g. "my_rpkg/*.tgz"

Local reference sequences (--local_ref)

A single path to one or several local fasta files containing orthologous groups of proteins. the referece sequences should be annotated with their taxonomy ID in the NCBI taxonomy (e.g. 562.NC_011750 as the sequence record’s header, 562 being the taxID).

Output options

Output queries (--queries_dir)

Output directory for queries; assembled contigs, placement results and summary tables/figures get saved here. Defaults to queries.

Output references (--reference_dir)

Output directory for references; fasta files, alignments, model files and trees get saved here. Defaults to references.

Run parameters

Phylogenetic method (--phylo_method)

Phylogentic tool used for the reconstruction of the reference tree. Only used for references from EggNOG and local files, not packages. Accepted values: iqtree, fasttree, raxml.

Alignment method (--align_method)

Alignment tool used to compute reference alignments. Only used for references from EggNOG and local files, not packages. Accepted values: maftt-*, prank.

Taxonomic lineage (--lineage)

the lineage(s) to report occurences for. Can be either a list of labels provided by the user (e.g. Rickettsiales,Holosporales), a taxonmic rank (e.g. family), or both (e.g. Rickettsia,family)

No. of CPUs (--cpus)

No. of CPUs to use. For more fine-grained uage of resources per process change the file nextflow.config.

Threshold for plotting taxonomic labels (--plot_threshold)

Threshold for filtering low frequent taxon labels from summary plots. e.g. label would not get plotted when present in only 1 out of 4 trees for default value. Threshold is checked per sample. Default: 0.25, accepted values between o and 1

Threshold for including taxonomic labels (--aLWR_threshold)

Threshold of accumulated likelihood weight ratio (aLWR, see gappa’s documentation) to include labels in the summary table. Default 0.8, accepted values between o and 1

MEGAN VM options file (--megan_vmoptions)

File with options that are passed on to the Java virtual machine running MEGAN. Most importantly, state here the amount of memory that is available, e.g. -Xmx16G for 16GB. By default the file is expected to be in the execution directory. Example file MEGAN.vmoptions is included in the repository.

Location of MEGAN (--megan_dir)

The directory MEGAN’s source files are located. When Manually installing MEGAN it could be something like /usr/local/megan. Leave as default if the singularity image is used.

Location of Python3 (--python3)

Location of the python3 executable that has all needed packages available. Should usually be /usr/bin/env python3, leave as default is using the singularity image.