Run Eukfinder for Long reads or MAGs - dzhao2019/Eukfinder-Test GitHub Wiki

usage

 Eukfinder long_seqs [-h] -l LONG_SEQS -o OUT_NAME --mhlen MHLEN --cdb
                            CDB -n NUMBER_OF_THREADS -z NUMBER_OF_CHUNKS -t
                            TAXONOMY_UPDATE -p PLAST_DATABASE -m PLAST_ID_MAP
                            -a ACC2TAX_DATABASE -e E_VALUE --pid PID --cov COV

optional arguments:

-h, --help show this help message and exit

Required arguments:

Description

-l LONG_SEQS, --long-seqs LONG_SEQS long sequences file

-o OUT_NAME, --out_name OUT_NAME out name

--mhlen MHLEN, --min-hit-length MHLEN minimum hit length

--cdb CDB, --centrifuge-database CDB path to centrifuge database

-n NUMBER_OF_THREADS, --number-of-threads NUMBER_OF_THREADS Number of threads

-z NUMBER_OF_CHUNKS, --number-of-chunks NUMBER_OF_CHUNKS Number of chunks to split a file

-t TAXONOMY_UPDATE, --taxonomy-update TAXONOMY_UPDATE Set to True the first time the program is used. Otherwise set to False

-p PLAST_DATABASE, --plast-database PLAST_DATABASE path to plast database

-m PLAST_ID_MAP, --plast-id-map PLAST_ID_MAP path to taxonomy map for plast database

-a ACC2TAX_DATABASE, --acc2tax-database ACC2TAX_DATABASE path to acc2tax database

-e E_VALUE, --e-value E_VALUE threshold for plast searches

--pid PID, --percent_id PID percentage identity for plast searches

--cov COV, --coverage COV percentage coverage for plast searches

shell example

#!/bin/bash

#$ -S /bin/bash

. /etc/profile

#$ -cwd

#$ -pe threaded 20

cd $PWD

input=your-contings.fasta

prefix=your_outname

# path to databases

plastdb=PlastDB_Jun2020.fasta.nal

plastmap=PlastDB_Jun2020_map.txt

centrifuge=Centrifuge_NewDB_Sept2020

acc2tax=Acc2Tax_Feb122021/

python eukfinder.py long_seqs -l $input -n 48 -z 6 --mhlen 100 -t False \

      -p $plastdb -m $plastmap -a $acc2tax -e 0.01 --pid 60 --cov 30 -o $prefix --cdb $centrifuge

# Use 'eukfinder.py long_seqs -h ' for help message

# Set '-t T' if it is the first time the program is used