Difference between revisions of "FALCON fc run cfg"
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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. |
Download the raw [{{#fileLink: fc_run.cfg}} fc_run.cfg] file. | Download the raw [{{#fileLink: fc_run.cfg}} fc_run.cfg] file. | ||
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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 = | + | 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 | sge_option_da = --ntasks 1 --nodes 1 --cpus-per-task 8 --mem 3000 --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 | sge_option_la = --ntasks 1 --nodes 1 --cpus-per-task 2 --mem 500 --time 00:05:00 --account=%(group)s --qos=%(group)s-b | ||
Revision as of 02:56, 27 May 2016
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.
Download the raw [{{#fileLink: fc_run.cfg}} fc_run.cfg] file. {{#fileAnchor: fc_run.cfg}}
[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 8 --mem 3000 --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
sge_option_pda = --ntasks 1 --nodes 1 --cpus-per-task 8 --mem 11000 --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
sge_option_fc = --ntasks 1 --nodes 1 --cpus-per-task 16 --mem 1000 --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
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