FALCON fc large run cfg
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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.
[General] 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 group = GROUPNAME 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