ctg_align failed

[jjssuuhh]

Describe the bug
i got some error

Error message
[17613 ERROR] 2024-02-14 06:28:37 ctg_align failed: please check the following logs:
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align01/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align02/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align07/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align08/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align09/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align11/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align12/nextDenovo.sh.e
[17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align13/nextDenovo.sh.e

and i check the file

hostname

• hostname
  cd /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align01
• cd /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align01
  time /var2/home/sejung/miniconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/minimap2-nd --step 3 -x map-ont -t 80 -x map-ont -a -t 80 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/./NextDenovorunned/01.raw_align/input.seed.001.2bit|/var2/home/sejung/miniconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/bam_sort -i -@ 80 -o input.seed.001.2bit.sort.bam
• /var2/home/sejung/miniconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/minimap2-nd --step 3 -x map-ont -t 80 -x map-ont -a -t 80 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/./NextDenovorunned/01.raw_align/input.seed.001.2bit
• /var2/home/sejung/miniconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/bam_sort -i -@ 80 -o input.seed.001.2bit.sort.bam
  [M::mm_idx_gen::69.6672.01] collected minimizers
  [M::mm_idx_gen::108.3071.83] sorted minimizers
  [M::main::108.3071.83] loaded/built the index for 1502 target sequence(s)
  [M::mm_mapopt_update::110.7781.81] mid_occ = 1070
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1502
  [M::mm_idx_stat::112.243*1.80] distinct minimizers: 71654870 (51.55% are singletons); average occurrences: 4.493; average spacing: 5.307
  samtools sort: couldn't allocate memory for bam_mem

Genome characteristics
genome size option was 1.44G

[Hu Jiang]

It seems that the thread parameter (80) you set is too large, which consumes too much memory and crashed. So please reduce this value.

[jjssuuhh]

[General]
job_type = local
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 10
input_type = raw
read_type = ont
input_fofn = ./input.fofn
workdir = ./NextDenovorunned

[correct_option]
read_cutoff = 1k
genome_size = 1.44g
seed_cutoff = 13966
blocksize = 10g
pa_correction = 15
seed_cutfiles = 5
sort_options = -m 40g -t 80 -k 60
minimap2_options_raw = -x ava-ont -t 80
correction_options = -p 80 -b

[assemble_option]
minimap2_options_cns = -x ava-ont -t 80 -k17 -w17
minimap2_options_map = -x map-ont -t 80
nextgraph_options = -a 1

this is my run.cfg file, should i have to remove sort_options -t 80? or every -t 80?

[Hu Jiang]

try minimap2_options_map = -x map-ont -t 20

[jjssuuhh]

thankyou!! l will try that!