Run Manually

Alternatively, you can run scripts/cnidaria.py, the main program, for the analysis.

$ scripts/cnidaria.py -h

6
cnidaria version: 8
build date      : Mar 31 2016
build time      : 11:12:50
usage: cnidaria.py [-h] [-out [OUT_FILE]] [-thr [NUM_THREADS]] [-min [MINVAL]]
                   [-se [SAVE_EVERY]] [-np [NUM_PIECES]] [-pn [PIECE_NUM]]
                   [-n] [-d] [-me] [-nm] [-ec] [-nem]
                   infiles [infiles ...]

Cnidaria Merger

positional arguments:
  infiles               Input Jellyfish databases

optional arguments:
  -h, --help            show this help message and exit
  -out [OUT_FILE], --outfile [OUT_FILE]
                        Prefix of output file (default: cnidaria_db)
  -thr [NUM_THREADS], --threads [NUM_THREADS]
                        Number of threads. Not compatible with COMPLETE
                        (default: 1)
  -min [MINVAL], --min-val [MINVAL]
                        Minimum number of shared species to start counting
                        (default: 2)
  -se [SAVE_EVERY], --save-every [SAVE_EVERY]
                        Count every N k-mers. Speeds analysis while skipping
                        data (default: 1)
  -np [NUM_PIECES], --num-pieces [NUM_PIECES]
                        Number of pieces (default: 1)
  -pn [PIECE_NUM], --piece-num [PIECE_NUM]
                        Piece number (default: None)
  -n, -dry, --dry-run   Dry run (default: False)
  -d, -dump, --dump-only
                        Dump only (default: False)
  -me, -merge, --merge-only
                        Merge only (default: False)
  -nm, -nomerge, --do-not-merge
                        Do not merge (default: True)
  -ec, -complete, --export-complete
                        Export COMPLETE database (default: False)
  -nem, -nomatrix, --no-export-matrix
                        DO NOT Export MATRIX database (default: True)

complete - create complete datavase (CNE) file - useful to merge extra data and for filtering analysis NUM_THREADS - Number of threads to run if in quick analysis mode (no complete) NUM_PIECES - Number of pieces to run in quick analysis mode or complete mode.

if running in complete mode

cnidaria.py --num-pieces 3 --piece-num 1 --outfile cnidaria_db <F1.jf> <F2.jf> <F3.jf> <F4.jf> &
cnidaria.py --num-pieces 3 --piece-num 2 --outfile cnidaria_db <F1.jf> <F2.jf> <F3.jf> <F4.jf> &
cnidaria.py --num-pieces 3 --piece-num 3 --outfile cnidaria_db <F1.jf> <F2.jf> <F3.jf> <F4.jf> &

This will run the analysis in 3 pieces. generating:

cnidaria_db_0001_0003.cnm
cnidaria_db_0001_0003.cne
cnidaria_db_0001_0003.json
cnidaria_db_0001_0003.log
cnidaria_db_0002_0003.cnm
cnidaria_db_0002_0003.cne
cnidaria_db_0002_0003.json
cnidaria_db_0002_0003.log
cnidaria_db_0003_0003.cnm
cnidaria_db_0003_0003.cne
cnidaria_db_0003_0003.json
cnidaria_db_0003_0003.log

when finished, run:

cnidaria.py --num-pieces 3 --merge-only  --outfile cnidaria_db <F1.jf> <F2.jf> <F3.jf> <F4.jf>

which will merge the files into a single file:

cnidaria_db.cnm
cnidaria_db.cne
cnidaria_db.json
cnidaria_db.log

CNE will only be generated if you ask for the complete database