pyani fastani

The fastani subcommand will carry out fastANI analysis using genome files contained in the indir directory, writing result files to the outdir directory, and recording data about each comparison and run in a local SQLite3 database.

usage: pyani fastani [-h] [-l LOGFILE] [-v] [--debug]
              [--disable_tqdm] [--citation] [--scheduler {multiprocessing,SGE}]
              [--workers WORKERS] [--SGEgroupsize SGEGROUPSIZE]
              [--SGEargs SGEARGS] [--jobprefix JOBPREFIX] [--name NAME]
              [--classes CLASSES] [--labels LABELS] [--recovery]
              [--dbpath DBPATH] [--fastani_exe FASTANI_EXE] [-k KMERSIZE]
              [--fragLen FRAGLEN] [-t THREADS] [--minFraction MINFRACTION]
              -i INDIR -o OUTDIR

Flagged arguments

-i, --input INDIR

Path to the directory containing indexed genome files to be used for the analysis.

-o, --outdir OUTDIR

Path to a directory where comparison output files will be written.

--classes CLASSFNAME

Use the set of classes (one per genome sequence file) found in the file CLASSFNAME in INDIR. Default: classes.txt

--dbpath DBPATH

Path to the location of the local pyani database to be used. Default: .pyani/pyanidb

--disable_tqdm

Disable the tqdm progress bar while the download process runs. This is useful when testing to avoid aesthetic problems with test output.

--fastani_exe FASTANI_EXE

Path to the fastANI executable. Default: fastANI

--fragLen FRAGLEN

Fragment length to use in analysis. (default: 3000)

-h, --help

Display usage information for pyani fastani.

--jobprefix JOBPREFIX

Use the string JOBPREFIX as a prefix for SGE job submission names. Default: PYANI

-k, --kmer KMERSIZE

Set the kmer size <= 16; can not be greater than 16. (default: 16)

--labels LABELFNAME

Use the set of labels (one per genome sequence file) found in the file LABELFNAME in INDIR. Default: labels.txt

-l LOGFILE, --logfile LOGFILE

Provide the location LOGFILE to which a logfile of the download process will be written.

--minFraction MINFRACTION

Minimum fraction of genome that must be shared for trusting ANI. If reference and query genome size differ, smaller one among the two is considered. (default: 0.2)

--name NAME

Use the string NAME to identify this fastANI run in the pyani database.

--recovery

Use existing fastANI comparison output if available, e.g. if recovering from a failed job submission. Using this option will not generate a new comparison if the old output files exist.

--scheduler {multiprocessing, SGE}

Specify the job scheduler to be used when parallelising genome comparisons: one of multiprocessing (use many cores on the current machine) or SGE (use an SGE or OGE job scheduler). Default: multiprocessing.

--SGEargs SGEARGS

Pass additional arguments SGEARGS to qsub when running the SGE-distributed jobs.

--SGEgroupsize SGEGROUPSIZE

Create SGE arrays containing SGEGROUPSIZE comparison jobs. Default: 10000

-v, --verbose

Provide verbose output to STDOUT.

--workers WORKERS

Spawn WORKERS worker processes with the --scheduler multiprocessing option. Default: 0 (use all cores)