“stop” at the cns_align step

[WenhaoLiu0218]

Dear authors, i used nextdenovo to run genome assembly (the genome size is about 1GB, raw data size is about 100G), it looks like "stopping" at the cns_align step, since the file (cns.filt.dovt.ovl and cns.filt.dovt.ovl.bl) in 01_rundir/02.cns_align/02.cns_align.sh.work/cns_align* is still keep empty, however, the software has been ran this step for 5 days with the CPU time keep increscing. The same issue occured when i changed to the older version. I don't know what is the problem for it, not enough CPU to run it (i use 10 CPU cores to run it and the SGE monitor shows the vmem is always keep at about 500G) or for some other reasons? it would be very appreciate if i can get your help!

here is my run.cfg: [General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 20 input_type = raw input_fofn = input.fofn workdir = 01_rundir [correct_option] read_cutoff = 1k seed_cutoff = 9k (the result of bin/seq_stat, conf: -g 1GB, -d 50) blocksize = 2g pa_correction = 20 seed_cutfiles = 20 sort_options = -m 20g -t 10 -k 50 minimap2_options_raw = -x ava-pb -t 8 correction_options = -p 15 [assemble_option] minimap2_options_cns = -x ava-pb -t 8 -k17 -w17 nextgraph_options = -a 1

and the end of the nextDenovo.sh.e file in cns_align000: [M::mm_idx_gen::51.1031.14] collected minimizers [M::mm_idx_gen::62.5411.16] sorted minimizers [M::main::62.5411.16] loaded/built the index for 57675 target sequence(s) [M::mm_mapopt_update::63.0311.16] mid_occ = 2742 [M::mm_idx_stat] kmer size: 17; skip: 17; is_hpc: 1; #seq: 57675 [M::mm_idx_stat::63.336*1.15] distinct minimizers: 11002036 (26.52% are singletons); average occurrences: 8.938; average spacing: 11.761

GCC What version of GCC are you using? 7.4.0 (GCC)

Python What version of Python are you using? 2.7.9

NextDenovo What version of NextDenovo are you using? v2.3.0

[moold]

Try minimap2_options_cns = -x ava-pb -t 8 -k17 -w17 --mode 1

[WenhaoLiu0218]

Hi, Thanks for your reply to our question, we added the parameter "--mode 1" which change the slow mode to fast mode, but the file is still empty for about 5 days.

[moold]

Could you share the two input files with me? I need the input files to check what happened?

[WenhaoLiu0218]

Sorry for applying late, finally, we spend about 1.5 months to run this step, so it's just very slow. We have already finished the final assembly, thanks very much!