mseetin
commented
8 years ago Your issues are almost the number of concurrent jobs and -M. The daligner jobs use 4 cores each by default, so unless you have 192 cores in this system, that's probably too high to begin with. Also, your -M480 flag lets daligner use as much as 480 GB per job. If you use -M32, which we use internally most of the time, then you'd need to turn down your concurrent jobs to under 15. That may still be too taxing on your system, depending on it file i/o capabilities, so if you're still struggling to get this to run, try turning down the number of concurrent jobs some more.
Also, don't use --min_cov 20 unless you're using an abnormally large amount of coverage in this assembly. We most often use 2, but if you want to be more cautious about misassembly, use 3-5.
On Mon, Apr 18, 2016 at 2:32 AM, lauraalazar notifications@github.com wrote:
I needed to stop falcon because it was filling the memory. Here is my fc_run.cfg (for a genome of size ~150Mb and a computer with 500GB memory):
[General] job_type=local
list of files of the initial subread fasta files
input_fofn = input.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
Cluster queue setting
sge_option_da = sge_option_la = sge_option_pda = sge_option_pla = sge_option_fc = sge_option_cns =
concurrency settgin
pa_concurrent_jobs = 48 cns_concurrent_jobs = 48 ovlp_concurrent_jobs = 48
overlapping options for Daligner
pa_HPCdaligner_option = -v -dal128 -e.70 -l1000 -s1000 -M480 ovlp_HPCdaligner_option = -v -dal128 -h60 -e.96 -l500 -s1000 -M480
pa_DBsplit_option = -x500 -s400 ovlp_DBsplit_option = -x500 -s400
error correction consensus optione
falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 2 --max_n_read 200 --n_core 6
overlap filtering options
overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10
I would really appreciate comments on : 1) How can I resume falcon to finish what it was doing (folder 1-preads_ovl is still empty)? 2) What set of parameters would avoid filling the memory? More generally, do the parameters I'm using make sense?
Thanks!
— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/PacificBiosciences/FALCON/issues/336
pb-cdunn
lauraalazar
I needed to stop falcon because it was filling the memory. Here is my fc_run.cfg (for a genome of size ~150Mb and a computer with 500GB memory):
[General]job_type=local# list of files of the initial subread fasta filesinput_fofn = input.fofninput_type = raw#input_type = preads# The length cutoff used for seed reads used for initial mappinglength_cutoff = 12000# The length cutoff used for seed reads usef for pre-assemblylength_cutoff_pr = 12000# Cluster queue settingsge_option_da =sge_option_la =sge_option_pda =sge_option_pla =sge_option_fc =sge_option_cns =# concurrency settginpa_concurrent_jobs = 48cns_concurrent_jobs = 48ovlp_concurrent_jobs = 48# overlapping options for Dalignerpa_HPCdaligner_option = -v -dal128 -e.70 -l1000 -s1000 -M480ovlp_HPCdaligner_option = -v -dal128 -h60 -e.96 -l500 -s1000 -M480pa_DBsplit_option = -x500 -s400ovlp_DBsplit_option = -x500 -s400# error correction consensus optionefalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 2 --max_n_read 200 --n_core 6# overlap filtering optionsoverlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10I would really appreciate comments on : 1) How can I resume falcon to finish what it was doing (folder 1-preads_ovl is still empty)? 2) What set of parameters would avoid filling the memory? More generally, do the parameters I'm using make sense?
Thanks!