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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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Stop at ctg_graph, and no nd.asm.fasta.stat file #214

Open rubbyai opened 2 weeks ago

rubbyai commented 2 weeks ago

Describe the bug There is no error message, but stop at ctg_graph, and the nd.asm.fasta.stat file is empty.

Error message $cat pid397038.log.info [397038 INFO] 2024-09-19 14:50:39 NextDenovo start... [397038 INFO] 2024-09-19 14:50:39 version:2.5.2 logfile:pid397038.log.info [397038 WARNING] 2024-09-19 14:50:39 Re-write workdir [397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir [397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir/01.raw_align [397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir/02.cns_align [397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir/03.ctg_graph [397038 INFO] 2024-09-19 14:50:44 Total jobs: 1 [397038 INFO] 2024-09-19 14:50:44 Submitted jobID:[397101] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 14:53:35 db_stat done [397038 INFO] 2024-09-19 14:53:35 updated options: rerun: 3 task: all deltmp: 1 rewrite: 1 read_type: clr job_type: local input_type: raw read_cutoff: 1k parallel_jobs: 2 seed_depth: 45.0 pa_correction: 2 seed_cutfiles: 3 seed_cutoff: 31467 genome_size: 308161 job_prefix: nextDenovo blocksize: 21254056928 ctg_cns_options: -p 15 nextgraph_options: -a 1 sort_options: -m 1g -t 2 -k 40 minimap2_options_map: -x map-pb minimap2_options_raw: -t 8 -x ava-pb workdir: /DATA/User/wangyuru/nd_test/./01_rundir input_fofn: /DATA/User/wangyuru/nd_test/./input.fofn raw_aligndir: /DATA/User/wangyuru/nd_test/./01_rundir/01.raw_align cns_aligndir: /DATA/User/wangyuru/nd_test/./01_rundir/02.cns_align ctg_graphdir: /DATA/User/wangyuru/nd_test/./01_rundir/03.ctg_graph correction_options: -p 15 -max_lq_length 1000 -r clr -min_len_seed 15733 minimap2_options_cns: -t 8 -x ava-pb -k 17 -w 17 --minlen 2000 --maxhan1 5000 [397038 INFO] 2024-09-19 14:53:35 summary of input data: file: /DATA/User/wangyuru/nd_test/./01_rundir/01.raw_align/input.reads.stat [Read length stat] Types Count (#) Length (bp) N10 92896 11914 N20 231831 8963 N30 409363 7193 N40 627599 5901 N50 892600 4873 N60 1213882 4001 N70 1608923 3228 N80 2104007 2531 N90 2760865 1818

Types Count (#) Bases (bp) Depth (X) Raw 4715834 14758686284 47892.78 Filtered 934723 576114420 1869.52 Clean 3781111 14182571864 46023.25

Suggested seed_cutoff (genome size: 0.31Mb, expected seed depth: 45, real seed depth: 45.00): 31467 bp [397038 INFO] 2024-09-19 14:53:40 Total jobs: 1 [397038 INFO] 2024-09-19 14:53:40 Submitted jobID:[399041] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/02.db_split.sh.work/db_split1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 14:56:51 db_split done [397038 INFO] 2024-09-19 14:56:51 Total jobs: 9 [397038 INFO] 2024-09-19 14:56:51 Submitted jobID:[401236] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 14:56:51 Submitted jobID:[401242] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align2/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 14:56:54 Submitted jobID:[401326] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align3/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 14:56:56 Submitted jobID:[401380] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align4/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 14:56:59 Submitted jobID:[401434] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align5/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:02:22 Submitted jobID:[405678] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align6/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:02:25 Submitted jobID:[405732] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align7/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:02:28 Submitted jobID:[405797] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align8/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:03:00 Submitted jobID:[406341] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align9/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:08:25 raw_align done [397038 INFO] 2024-09-19 15:08:30 Total jobs: 3 [397038 INFO] 2024-09-19 15:08:30 Submitted jobID:[410287] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:08:30 Submitted jobID:[410307] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align2/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:09:02 Submitted jobID:[410666] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align3/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:09:33 sort_align done [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.002.2bit.3.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.002.2bit.6.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align8/input.seed.002.2bit.7.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align9/input.seed.002.2bit.8.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align1/input.seed.003.2bit.0.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align2/input.seed.003.2bit.1.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.003.2bit.2.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.003.2bit.3.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.001.2bit.2.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align5/input.seed.001.2bit.4.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align6/input.seed.001.2bit.5.ovl [397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.001.2bit.6.ovl [397038 INFO] 2024-09-19 15:09:38 Total jobs: 3 [397038 INFO] 2024-09-19 15:09:38 Submitted jobID:[411080] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:09:39 Submitted jobID:[411086] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns2/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:09:55 Submitted jobID:[411294] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns3/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:10 seed_cns done [397038 INFO] 2024-09-19 15:10:10 seed_cns finished, and final corrected reads file: [397038 INFO] 2024-09-19 15:10:10 /DATA/User/wangyuru/nd_test/./01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns/cns.fasta [397038 INFO] 2024-09-19 15:10:10 Total jobs: 6 [397038 INFO] 2024-09-19 15:10:10 Submitted jobID:[411487] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:10 Submitted jobID:[411503] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align2/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:21 Submitted jobID:[411672] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align3/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:23 Submitted jobID:[411714] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align4/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:26 Submitted jobID:[411778] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align5/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:30 Submitted jobID:[411852] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align6/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:35 cns_align done [397038 INFO] 2024-09-19 15:10:40 Total jobs: 1 [397038 INFO] 2024-09-19 15:10:40 Submitted jobID:[411993] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh] in the local_cycle. [397038 INFO] 2024-09-19 15:10:41 ctg_graph done ~/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align0/nextDenovo.sh.e

Genome characteristics droper sheep, the whole genome is about 2.6GB

Input data sheep cyclone data: file1: total base count 1281725586 file2: total base count 2110087581

Config file $cat run.cfg [General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 2 input_type = raw read_type = clr input_fofn = ./input.fofn workdir = ./01_rundir

[correct_option] read_cutoff = 1k genome_size = 308161 pa_correction = 2 sort_options = -m 1g -t 2 minimap2_options_raw = -t 8 correction_options = -p 15

[assemble_option] minimap2_options_cns = -t 8 nextgraph_options = -a 1

Operating system Which operating system and version are you using? No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.1 LTS Release: 22.04 Codename: jammy

GCC What version of GCC are you using? gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)

Python What version of Python are you using? Python 3.12.2

NextDenovo What version of NextDenovo are you using? nextDenovo 2.5.2

moold commented 1 week ago

genome_size = 308161, is this genome size (bp) correct?