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Description
Hello,
I am running NextDenovo with PacBio HiFi reads of a 35 Mb genome. I have been able to produce the fasta file of the assembly but I am getting an error when I try to obtain the assembly in gfa format. I have set the nextgraph_options = -a 3. Here is the run.cfg file
[General]
job_type = local # local, slurm, sge, pbs, lsf
job_prefix = nextDenovo_gfa
task = all # all, correct, assemble
rewrite = yes # yes/no
deltmp = yes
parallel_jobs = 1 # number of tasks used to run in parallel
input_type = raw # raw, corrected
read_type = hifi # clr, ont, hifi
input_fofn = input.fofn
workdir = ./gfa/
[correct_option]
read_cutoff = 1k
genome_size = 35m # estimated genome size
sort_options = -m 3g -t 28
minimap2_options_raw = -t 28
pa_correction = 3 # number of corrected tasks used to run in parallel, each corrected task requires ~TOTAL_INPUT_BASES/4 bytes of memory usage.
correction_options = -p 28
[assemble_option]
minimap2_options_cns = -t 28
nextgraph_options = -a 3 # GFA
Then I find a .gfa file at ./gfa/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.gfa but this gfa file only contains ten 7 bp contigs.
I am looking at the wrong file?
Here is the nextDenovo log for reference:
[1618 INFO] 2025-05-23 13:05:31 NextDenovo start...
[1618 INFO] 2025-05-23 13:05:31 version:2.5.2 logfile:pid1618.log.info
[1618 WARNING] 2025-05-23 13:05:31 Re-write workdir
[1618 INFO] 2025-05-23 13:05:31 mkdir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa/
[1618 INFO] 2025-05-23 13:05:31 mkdir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//01.raw_align
[1618 INFO] 2025-05-23 13:05:31 mkdir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//02.cns_align
[1618 INFO] 2025-05-23 13:05:31 mkdir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//03.ctg_graph
[1618 INFO] 2025-05-23 13:05:36 Total jobs: 1
[1618 INFO] 2025-05-23 13:05:36 Submitted jobID:[1644] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:06:28 db_stat done
[1618 INFO] 2025-05-23 13:06:28 updated options:
rerun: 3
task: all
deltmp: 1
rewrite: 1
job_type: local
input_type: raw
read_cutoff: 1k
read_type: hifi
parallel_jobs: 1
seed_depth: 40.0
pa_correction: 1
seed_cutfiles: 3
genome_size: 35m
seed_cutoff: 27249
blocksize: 16065496120
job_prefix: nextDenovo_gfa
ctg_cns_options: -sp -p 28
nextgraph_options: -a 3 -R 0.7
sort_options: -m 3g -t 28 -k 40
minimap2_options_map: -x asm20
minimap2_options_raw: -t 28 -x ava-hifi -f 800
correction_options: -p 28 -max_lq_length 1000 -r hifi
minimap2_options_cns: -t 28 -x ava-hifi --minide 0.1 --maxhan1 1000
workdir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa/
input_fofn: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/input.fofn
raw_aligndir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//01.raw_align
cns_aligndir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//02.cns_align
ctg_graphdir: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//03.ctg_graph
[1618 INFO] 2025-05-23 13:06:28 summary of input data:
file: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//01.raw_align/input.reads.stat
[Read length stat]
Types Count (#) Length (bp)
N10 19798 30754
N20 43159 27431
N30 68886 25244
N40 96628 23526
N50 126305 22040
N60 157966 20663
N70 191741 19360
N80 227858 18052
N90 266773 16636
Types Count (#) Bases (bp) Depth (X)
Raw 311411 6754832040 193.00
Filtered 0 0 0.00
Clean 311411 6754832040 193.00
*Suggested seed_cutoff (genome size: 35.00Mb, expected seed depth: 40, real seed depth: 40.00): 27249 bp
[1618 INFO] 2025-05-23 13:06:33 Total jobs: 1
[1618 INFO] 2025-05-23 13:06:33 Submitted jobID:[1880] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/02.db_split.sh.work/db_split1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:12:57 db_split done
[1618 INFO] 2025-05-23 13:12:56 Total jobs: 9
[1618 INFO] 2025-05-23 13:12:56 Submitted jobID:[3519] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:14:21 Submitted jobID:[4202] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align2/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:14:32 Submitted jobID:[4317] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align3/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:14:47 Submitted jobID:[4445] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align4/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:15:02 Submitted jobID:[4572] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align5/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:16:26 Submitted jobID:[5261] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align6/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:16:38 Submitted jobID:[5377] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align7/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:16:53 Submitted jobID:[5506] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align8/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:18:17 Submitted jobID:[6195] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align9/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:18:29 raw_align done
[1618 INFO] 2025-05-23 13:18:34 Total jobs: 3
[1618 INFO] 2025-05-23 13:18:34 Submitted jobID:[6331] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/04.sort_align.sh.work/sort_align1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:18:40 Submitted jobID:[6382] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/04.sort_align.sh.work/sort_align2/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:18:46 Submitted jobID:[6431] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/04.sort_align.sh.work/sort_align3/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:18:52 sort_align done
[1618 INFO] 2025-05-23 13:18:52 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align1/input.seed.001.2bit.0.ovl
[1618 INFO] 2025-05-23 13:18:52 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align2/input.seed.001.2bit.1.ovl
[1618 INFO] 2025-05-23 13:18:52 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.001.2bit.2.ovl
[1618 INFO] 2025-05-23 13:18:52 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.001.2bit.3.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.002.2bit.2.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align5/input.seed.002.2bit.4.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align6/input.seed.002.2bit.5.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.002.2bit.6.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.003.2bit.3.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.003.2bit.6.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align8/input.seed.003.2bit.7.ovl
[1618 INFO] 2025-05-23 13:18:53 remove temporary result: /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/01.raw_align/03.raw_align.sh.work/raw_align9/input.seed.003.2bit.8.ovl
[1618 INFO] 2025-05-23 13:18:58 Total jobs: 3
[1618 INFO] 2025-05-23 13:18:58 Submitted jobID:[6502] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/01.seed_cns.sh.work/seed_cns1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:21:48 Submitted jobID:[7205] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/01.seed_cns.sh.work/seed_cns2/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:24:36 Submitted jobID:[7897] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/01.seed_cns.sh.work/seed_cns3/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:27:24 seed_cns done
[1618 INFO] 2025-05-23 13:27:24 seed_cns finished, and final corrected reads file:
[1618 INFO] 2025-05-23 13:27:24 /mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/./gfa//02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta
[1618 INFO] 2025-05-23 13:27:24 Total jobs: 6
[1618 INFO] 2025-05-23 13:27:24 Submitted jobID:[8590] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/02.cns_align.sh.work/cns_align1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:27:33 Submitted jobID:[8694] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/02.cns_align.sh.work/cns_align2/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:27:45 Submitted jobID:[8811] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/02.cns_align.sh.work/cns_align3/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:27:58 Submitted jobID:[8928] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/02.cns_align.sh.work/cns_align4/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:28:07 Submitted jobID:[9036] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/02.cns_align.sh.work/cns_align5/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:28:22 Submitted jobID:[9161] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/02.cns_align/02.cns_align.sh.work/cns_align6/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:28:32 cns_align done
[1618 INFO] 2025-05-23 13:28:37 Total jobs: 1
[1618 INFO] 2025-05-23 13:28:37 Submitted jobID:[9293] jobCmd:[/mnt/e/seq_data/2025_04_21_Ppax_genome/PPAX_nextdenovo/gfa/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo_gfa.sh] in the local_cycle.
[1618 INFO] 2025-05-23 13:28:39 ctg_graph done
[1618 INFO] 2025-05-23 13:28:39 nextDenovo finished
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