FALCON fc large run cfg

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back to the FALCON page This is an example FALCON-integrate fc_run.cfg script based on the ecoli test included with the distribution. Make sure to change the 'GROUPNAME' to your group name.

job_type = SLURM

# list of files of the initial bas.h5 files
input_fofn = input.fofn
#input_fofn = preads.fofn

input_type = raw
#input_type = preads

# The length cutoff used for seed reads used for initial mapping
length_cutoff = 12000

# The length cutoff used for seed reads usef for pre-assembly
length_cutoff_pr = 12000
sge_option_da = --ntasks=1 --nodes=1 --cpus-per-task=4 --mem=50gb --time=72:00:00 --account=%(group)s --qos=%(group)s-b
sge_option_la = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=5gb --time=72:00:00 --account=%(group)s --qos=%(group)s-b
sge_option_pda = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=24gb --time=72:00:00 --account=%(group)s --qos=%(group)s-b
sge_option_pla = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=5gb --time=72:00:00 --account=%(group)s --qos=%(group)s-b
sge_option_fc = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=10gb --time=72:00:00 --account=%(group)s --qos=%(group)s-b
sge_option_cns = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=12gb --time=72:00:00 --account=%(group)s --qos=%(group)s-b

pa_concurrent_jobs = 16
ovlp_concurrent_jobs = 16

#OM: Set -M to 40 per https://github.com/thegenemyers/DALIGNER to avoid overflowing memory
pa_HPCdaligner_option =  -v -B128 -e0.70 -l1000 -s1000 -t5  -h35 -M40
ovlp_HPCdaligner_option = -v -B28 -e.96 -l500 -s1000 -t5 -h60

pa_DBsplit_option = -x500 -s800 -a
ovlp_DBsplit_option = -x500 -s800 -a

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 6

overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 --n_core 24