FALCON config for HGAP 4 002032/tasks/falcon_ns.tasks.task_falcon_gen_config-0/fc_run.cfg vs. FALCON conda fc_run_human.15kb.tweaked.cfg (in theory should be functionally the same)

fc_run.cfg

[General]
genome_size = 3200000000
pbsmrtpipe.hgap_aggressiveasm_bool = False
falcon_sense_greedy = False
falcon_sense_skip_contained = False
length_cutoff = -1
pbsmrtpipe.hgap_genomelength_str = 3200000000
pa_dbsplit_option = -a -x500 -s400
ovlp_hpcdaligner_option = -v -dal128  -M24 -k24 -h1024 -e.96 -l2500 -s100
seed_coverage = 30.0
falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 400 --n_core 12
pbsmrtpipe.hgap_seedcoverage_str = 30
overlap_filtering_setting = --max_diff 40 --max_cov 80 --min_cov 2 --n_core 12
pbsmrtpipe.hgap_seedlengthcutoff_str = -1
length_cutoff_pr = 15000
ovlp_dbsplit_option = -s400
pa_hpcdaligner_option = -v -dal128 -t16 -e0.75 -M24 -l4800 -k18 -h480 -w8 -s100

fc_run_human.15kb.tweaked.cfg

#### Input
[General]
input_fofn=input.fofn
input_type=raw
pa_DBdust_option=true
pa_fasta_filter_option=pass
target=assembly
skip_checks=False
LA4Falcon_preload=false

#### Data Partitioning
pa_DBsplit_option=-a -x500 -s400
ovlp_DBsplit_option=-s400

#### Repeat Masking
pa_HPCTANmask_option=
#no-op repmask param set
pa_REPmask_code=0,300;0,300;0,300

####Pre-assembly
# hgap uses -k18 -w8 -h480 -t16 -e0.75 -l4800
genome_size=3200000000
seed_coverage=30
length_cutoff=-1
pa_HPCdaligner_option=-v -B128 -M24
pa_daligner_option= -k18 -w8 -h480 -t16 -e0.75 -l4800 -s100
# hgap uses --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 400
falcon_sense_option=--output-multi --min-idt 0.70 --min-cov 4 --max-n-read 400
falcon_sense_greedy=False

####Pread overlapping
# hgap uses  -v -k24 -h1024 -H15000 -e0.96 -l2500 -M24
ovlp_HPCdaligner_option=-v -B128 -M24 
ovlp_daligner_option=-k24 -e.96 -l2500 -h1024 -s100

####Final Assembly
length_cutoff_pr=15000
overlap_filtering_setting=--max_diff 40 --max_cov 80 --min_cov 2
fc_ovlp_to_graph_option=

[job.defaults]
job_type=lsf
pwatcher_type=blocking
JOB_QUEUE=long
MB=32767
NPROC=6
njobs=300
submit = bsub -K \
  -q ${JOB_QUEUE}     \
  -J ${JOB_NAME}      \
  -o "${JOB_STDOUT}"  \
  -e "${JOB_STDERR}"  \
  -n ${NPROC}         \
  -M ${MB}            \
  -R 'select[mem>${MB}] rusage[mem=${MB}] span[hosts=1]' \
  "${JOB_SCRIPT}"

[job.step.da]
NPROC=4
MB=32767
njobs=300
[job.step.la]
NPROC=4
MB=32767
njobs=300
[job.step.cns]
NPROC=8
MB=65535
njobs=300
[job.step.pda]
NPROC=4
MB=32767
njobs=300
[job.step.pla]
NPROC=4
MB=32767
njobs=300
[job.step.asm]
NPROC=24
MB=196608
njobs=1