moold
commented
2 years ago It seems the error was caused by the computer cluster, so you can update NextDenovo to the latest version and try again.
Closed fengyuanli304 closed 1 year ago
moold
commented
2 years ago It seems the error was caused by the computer cluster, so you can update NextDenovo to the latest version and try again.
fengyuanli304
commented
2 years ago Hi, Dr. Hu Thank you for your reply. I update NextDenovo to the latest version and try again. I got the same error reported before: srun: error: Node failure on cn01 but nextDenovo2.4.sh.e says insufficient memory Could I deal with this problem by optimizing parallel computing parameters?
run.cfg: [General] job_type = local job_prefix = nextDenovo2.4 task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes parallel_jobs = 4 input_type = raw read_type = ont input_fofn = ./input.fofn workdir = ./
[correct_option] read_cutoff = 1k seed_cutoff = 25k genome_size = 900m blocksize = 1g pa_correction = 4 sort_options = -m 25g -t 5 minimap2_options_raw = -t 5 correction_options = -p 5
[assemble_option] minimap2_options_cns = -t 5 nextgraph_options = -a 1
hostname
Hi, Dr. Hu I try to assemble the genome of some species using NextDenovo, but one of them has an error. Thank you very much. Question or Expected behavior srun: error: Node failure on cn09.
Operating system Which operating system and version are you using? CentOS Linux release 7.5.1804 (Core).
GCC What version of GCC are you using? gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC)
Python What version of Python are you using? python 2.7.15
NextDenovo What version of NextDenovo are you using? nextDenovo 2.3.1
Additional context (Optional) run.cfg: [General] job_type = local job_prefix = nextDenovo2.3.1 task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 4 input_type = raw input_fofn = ./input.fofn workdir = ./
[correct_option] read_cutoff = 1k seed_cutoff = 25k genome_size = 900m blocksize = 1g pa_correction = 4 seed_cutfiles = 4 sort_options = -m 25g -t 5 -k 50 minimap2_options_raw = -x ava-ont -t 5 correction_options = -p 5
[assemble_option] minimap2_options_cns = -x ava-ont -t 5 -k17 -w17 nextgraph_options = -a 1
log: [INFO] 2021-09-14 15:29:12,162 start... [INFO] 2021-09-14 15:29:12,163 logfile: pid17926.log.info [WARNING] 2021-09-14 15:29:12,167 Re-write workdir [INFO] 2021-09-14 15:29:12,167 options: [INFO] 2021-09-14 15:29:12,167 {'sort_threads': 5, 'nodelist': '', 'rewrite': 1, 'blocksize': '1g', 'job_prefix': 'nextDenovo2.3.1', 'job_type': 'local', 'minimap2_options_map': ' -x map-ont', 'cns_threads': 5, 'map_threads': 5, 'sort_mem': '25g', 'seed_cutoff': '25000', 'input_fofn': '/gpfs/user/lifengyuan/data/nextdenovo_ot4/./input.fofn', 'read_cutoff': '1k', 'input_type': 'raw', 'sort_options': '-m 25g -t 5 -k 50', 'parallel_jobs': '4', 'cluster_options': '', 'sge_queue': '', 'ctg_graphdir': '/gpfs/user/lifengyuan/data/nextdenovo_ot4/.//03.ctg_graph', 'pa_correction': '4', 'genome_size': '900m', 'workdir': '/gpfs/user/lifengyuan/data/nextdenovo_ot4/./', 'minimap2_threads': (5, 5), 'minimap2_options_raw': '-x ava-ont -t 5', 'minimap2_options_cns': '-x ava-ont -t 5 -k17 -w17 --minlen 2000 --maxhan1 5000', 'cns_aligndir': '/gpfs/user/lifengyuan/data/nextdenovo_ot4/.//02.cns_align', 'seed_cutfiles': '4', 'raw_aligndir': '/gpfs/user/lifengyuan/data/nextdenovo_ot4/.//01.raw_align', 'task': 'all', 'ctg_cns_options': ' -p 5', 'deltmp': 1, '_random_round_with_less_accuracy': 0, 'rerun': 3, 'correction_options': '-p 5 -max_lq_length 10000 -min_len_seed 12500', 'nextgraph_options': '-a 1'} [INFO] 2021-09-14 15:29:12,167 skip mkdir: /gpfs/user/lifengyuan/data/nextdenovo_ot4/./ [INFO] 2021-09-14 15:29:12,168 mkdir: /gpfs/user/lifengyuan/data/nextdenovo_ot4/.//01.raw_align [INFO] 2021-09-14 15:29:12,168 mkdir: /gpfs/user/lifengyuan/data/nextdenovo_ot4/.//02.cns_align [INFO] 2021-09-14 15:29:12,169 mkdir: /gpfs/user/lifengyuan/data/nextdenovo_ot4/.//03.ctg_graph [INFO] 2021-09-14 15:29:12,170 analysis tasks done [INFO] 2021-09-14 15:29:17,184 total jobs: 1 [INFO] 2021-09-14 15:29:17,186 Throw jobID:[17941] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 15:52:24,926 db_split done [INFO] 2021-09-14 15:52:24,936 analysis tasks done [INFO] 2021-09-14 15:52:25,070 total jobs: 206 [INFO] 2021-09-14 15:52:25,071 Throw jobID:[19300] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align000/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 15:52:25,573 Throw jobID:[19305] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align001/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 15:52:26,076 Throw jobID:[19311] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align002/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 15:52:26,579 Throw jobID:[19322] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align003/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 16:25:05,782 Throw jobID:[21371] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align004/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 16:26:43,537 Throw jobID:[21480] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align005/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 16:28:10,917 Throw jobID:[21591] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align006/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 16:29:22,816 Throw jobID:[21678] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align007/nextDenovo2.3.1.sh] in the local_cycle. [INFO] 2021-09-14 16:29:23,636 Throw jobID:[21684] jobCmd:[/gpfs/user/lifengyuan/data/nextdenovo_ot4/01.raw_align/02.raw_align.sh.work/raw_align008/nextDenovo2.3.1.sh] in the local_cycle. srun: error: Node failure on cn09 srun: error: Node failure on cn09
/01.raw_align/02.raw_align.sh.work/raw_align008/nextDenovo2.3.1.sh.e hostname