falcon-2

too young too naive

falcon配置文件更改

[General]
#Input
input_fofn=input.fofn
input_type=raw
pa_DBdust_option=true
pa_fasta_filter_option=streamed-median



#Data Partitioning
# large genomes
# pa_DBsplit_option=-x500 -s200
# ovlp_DBsplit_option=-x500 -s200

# small genomes (<10Mb)
pa_DBsplit_option = -x500 -s50
ovlp_DBsplit_option = -x500 -s50



#Repeat Masking
pa_HPCTANmask_option=
pa_REPmask_code=0,300;0,300;0,300



#Pre-assembly
genome_size=10000000
seed_coverage=30
length_cutoff=-1    
pa_HPCdaligner_option=-v -B128 -M24
pa_daligner_option=-e0.8 -l2000 -k18 -h480  -w8 -s100
falcon_sense_option=--output-multi --min-idt 0.70 --min-cov 3 --max-n-read 400
falcon_sense_greedy=False


#Pread overlapping
ovlp_daligner_option=-e.96 -s1000 -h60
ovlp_HPCdaligner_option=-v -M24 -l500

#Final Assembly
overlap_filtering_setting=--max-diff 100 --max-cov 100 --min-cov 2
fc_ovlp_to_graph_option=
length_cutoff_pr=1000


#Miscellaneous configuration options
target=assembly
skip_checks=False
LA4Falcon_preload=false


#Job Distribution
[job.defaults]
#job_type=sge
job_type=local
pwatcher_type=blocking
#pwatcher_type=fs_based
JOB_QUEUE = all.q
MB = 32768
NPROC = 6
njobs = 32

submit =  /bin/bash -c "${JOB_SCRIPT}" > "${JOB_STDOUT}" 2> "${JOB_STDERR}"
#submit = qsub -S /bin/bash -sync y -V  \
#  -q ${JOB_QUEUE}     \
#  -N ${JOB_NAME}      \
#  -o "${JOB_STDOUT}"  \
#  -e "${JOB_STDERR}"  \
#  -l p= ${NPROC}    \
#  -l vf= ${MB}M   \
#  "${JOB_SCRIPT}"

[job.step.da]
NPROC=4
MB=49152
njobs=240