Difference between revisions of "FALCON fc run cfg"
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Moskalenko (talk | contribs) (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. | + | 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. |
| − | + | <pre> | |
| − | |||
| − | < | ||
[General] | [General] | ||
job_type = SLURM | job_type = SLURM | ||
| Line 21: | Line 19: | ||
# 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 = | + | group = GROUPNAME |
| − | sge_option_da = --ntasks 1 --nodes 1 --cpus-per-task | + | 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 | + | 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 | + | 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 | + | 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 | + | 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 | + | 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 | ||
| Line 42: | Line 40: | ||
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 | ||
| − | </ | + | </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