pb-cdunn
commented
6 years ago I installed the latest version of falcon
Meaning, a binary release? Something from Bioconda? This repo is out-of-date, as we no longer mirror our internal code-base here.
You should always test integration with the tiniest example possible. There is "synth0" in FALCON-examples for this purpose.
Hello I installed the latest version of falcon on my cluster and setting the parameters in cfg file suit for my genome(fish, 1.5~1.7G), but the program can't start succesfull and with no erro information in all.log. I don't know where is wrong in my cfg file or any thing else. This is my config file:
[General] job_type=lsf input_fofn = input.fofn input_type = raw length_cutoff = 10000 length_cutoff_pr = 15000 stop_all_jobs_on_failure = False target = assembly jobqueue = Sharedqueue sge_option_da = -n 5 -q %(jobqueue)s sge_option_la = -n 6 -q %(jobqueue)s sge_option_cns = -n 6 -q %(jobqueue)s sge_option_pda = -n 6 -q %(jobqueue)s sge_option_pla = -n 7 -q %(jobqueue)s sge_option_fc = -n 6 -q %(jobqueue)s
pa_concurrent_jobs = 200 cns_concurrent_jobs = 200 ovlp_concurrent_jobs = 200 pa_HPCdaligner_option = -v -B188 -t16 -w8 -M24 -e.75 -k18 -l4000 -s1000 ovlp_HPCdaligner_option = -v -B188 -t24 -M24 -k24 -h180 -e.96 -l2800 -s1000
pa_DBsplit_option = -x1000 -s250 -a ovlp_DBsplit_option = -x1000 -s250 falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 300 --n_core 8 overlap_filtering_setting = --max_diff 60 --max_cov 70 --min_cov 1 --bestn 10 --n_core 12 use_tmpdir = true use_tmpdir = /YZGROUP4/STORAGE/genewiz/genewiznj/Public
and this is all.log: all.log
this is mypwatcher dir output