Difference between revisions of "FALCON fc run cfg"

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(Created page with "back to the FALCON page Category:Software This is an example FALCON-integrate fc_run.cfg script. Download the raw [{{#fileLink: fc_run.cfg}} fc_run.cfg] file....")
 
 
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[[FALCON|back to the FALCON page]]
 
[[FALCON|back to the FALCON page]]
 
[[Category:Software]]
 
[[Category:Software]]
This is an example FALCON-integrate fc_run.cfg script.
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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 '<code>GROUPNAME</code>' to your group name.
  
Download the raw [{{#fileLink: fc_run.cfg}} fc_run.cfg] file.
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<pre>
{{#fileAnchor: run.sh}}
 
<source lang=make>
 
 
[General]
 
[General]
 
job_type = SLURM
 
job_type = SLURM
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# The length cutoff used for seed reads usef for pre-assembly
 
# The length cutoff used for seed reads usef for pre-assembly
 
length_cutoff_pr = 12000
 
length_cutoff_pr = 12000
group = CHANGE
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group = GROUPNAME
sge_option_da = --ntasks 1 --nodes 1 --cpus-per-task 8 --mem 3000 --time 00:20:00 --account=%(group)s --qos=%(group)s-b
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sge_option_da = --ntasks=1 --nodes=1 --cpus-per-task=4 --mem=5gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
sge_option_la = --ntasks 1 --nodes 1 --cpus-per-task 2 --mem 500 --time 00:05:00 --account=%(group)s --qos=%(group)s-b
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sge_option_la = --ntasks=1 --nodes=1 --cpus-per-task=2 --mem=1gb --time=00:05:00 --account=%(group)s --qos=%(group)s-b
sge_option_pda = --ntasks 1 --nodes 1 --cpus-per-task 8 --mem 11000 --time 00:20:00 --account=%(group)s--qos=%(group)s-b
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sge_option_pda = --ntasks=1 --nodes=1 --cpus-per-task=8 --mem=12gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
sge_option_pla = --ntasks 1 --nodes 1 --cpus-per-task 2 --mem 500 --time 00:05:00 --account=%(group)s --qos=%(group)s-b
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sge_option_pla = --ntasks=1 --nodes=1 --cpus-per-task=2 --mem=1gb --time=00:05:00 --account=%(group)s --qos=%(group)s-b
sge_option_fc = --ntasks 1 --nodes 1 --cpus-per-task 16 --mem 1000 --time 00:20:00 --account=%(group)s--qos=%(group)s-b
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sge_option_fc = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=3gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
sge_option_cns = --ntasks 1 --nodes 1 --cpus-per-task 8 --mem 9000 --time 00:20:00 --account=%(group)s--qos=%(group)s-b
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sge_option_cns = --ntasks=1 --nodes=1 --cpus-per-task=8 --mem=9gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
  
 
pa_concurrent_jobs = 32
 
pa_concurrent_jobs = 32
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overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 --n_core 24
 
overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 --n_core 24
  
</source>
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</pre>

Latest revision as of 20:31, 2 August 2021

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.

[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=5gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
sge_option_la = --ntasks=1 --nodes=1 --cpus-per-task=2 --mem=1gb --time=00:05:00 --account=%(group)s --qos=%(group)s-b
sge_option_pda = --ntasks=1 --nodes=1 --cpus-per-task=8 --mem=12gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
sge_option_pla = --ntasks=1 --nodes=1 --cpus-per-task=2 --mem=1gb --time=00:05:00 --account=%(group)s --qos=%(group)s-b
sge_option_fc = --ntasks=1 --nodes=1 --cpus-per-task=16 --mem=3gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b
sge_option_cns = --ntasks=1 --nodes=1 --cpus-per-task=8 --mem=9gb --time=00:20:00 --account=%(group)s --qos=%(group)s-b

pa_concurrent_jobs = 32
ovlp_concurrent_jobs = 32

pa_HPCdaligner_option =  -v -B4 -t16 -e.70 -l1000 -s1000
ovlp_HPCdaligner_option = -v -B4 -t32 -h60 -e.96 -l500 -s1000

pa_DBsplit_option = -x500 -s50
ovlp_DBsplit_option = -x500 -s50

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