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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

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#returned non-zero exit status 137, error info: .#

lide1993 opened this issue · comments

commented

Hi, Dr. Hu
I ran into this problem when I assembled the genome from ONT data and couldn't solve it:
Describe the bug
#returned non-zero exit status 137, error info: .#
hostname

  • hostname
    cd /home/victor/NextDenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align03
  • cd /home/victor/NextDenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align03
    time /home/victor/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -x ava-ont -t 4 /home/victor/NextDenovo/01_rundir/01.raw_align/input.seed.002.2bit /home/victor/NextDenovo/01_rundir/01.raw_align/input.part.004.2bit -o input.seed.002.2bit.2.ovl;
  • time /home/victor/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -x ava-ont -t 4 /home/victor/NextDenovo/01_rundir/01.raw_align/input.seed.002.2bit /home/victor/NextDenovo/01_rundir/01.raw_align/input.part.004.2bit -o input.seed.002.2bit.2.ovl
    Command terminated by signal 9
    136.84user 42.79system 10:54.44elapsed 27%CPU (0avgtext+0avgdata 16223296maxresident)k
    779264inputs+0outputs (19435major+12120401minor)pagefaults 0swaps

Genome characteristics
`genome size 336Mb,
[General]
job_type = local
job_prefix = nextDenovopomegranate0816
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 8
input_type = raw
read_type = ont
input_fofn = input.fofn
workdir = 01_rundir

[correct_option]
read_cutoff = 1k
genome_size = 336M
pa_correction = 3
sort_options = -m 3g -t 10
minimap2_options_raw = -x ava-ont -t 4
correction_options = -p 15

[assemble_option]
minimap2_options_cns = -x ava-ont -t 4 -k 21 -w 21
nextgraph_options = -a 1

commented

How much RAM does your computer have?

commented

How much RAM does your computer have?
hi，Dr. Hu
MemTotal: 98753020 kB
MemFree: 85963008 kB
MemAvailable: 96948512 kB
Buffers: 767056 kB
Cached: 10186696 kB
SwapCached: 17036 kB
Active: 1346316 kB
Inactive: 9709300 kB
Active(anon): 50588 kB
Inactive(anon): 44028 kB
Active(file): 1295728 kB
Inactive(file): 9665272 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 2097148 kB
SwapFree: 1806548 kB
Dirty: 0 kB
Writeback: 0 kB
AnonPages: 86196 kB
Mapped: 82792 kB
Shmem: 1200 kB
KReclaimable: 890620 kB
Slab: 1382476 kB
SReclaimable: 890620 kB
SUnreclaim: 491856 kB
KernelStack: 13200 kB
PageTables: 11728 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 51473656 kB
Committed_AS: 3832172 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 151228 kB
VmallocChunk: 0 kB
Percpu: 55808 kB
HardwareCorrupted: 0 kB
AnonHugePages: 0 kB
ShmemHugePages: 0 kB
ShmemPmdMapped: 0 kB
FileHugePages: 0 kB
FilePmdMapped: 0 kB
CmaTotal: 0 kB
CmaFree: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
Hugetlb: 0 kB
DirectMap4k: 2192244 kB
DirectMap2M: 97189888 kB
DirectMap1G: 3145728 kB

commented

Try the following config

parallel_jobs =1
pa_correction = 1
sort_options = -m 3g -t 30
minimap2_options_raw = -x ava-ont -t 32
correction_options = -p 30
minimap2_options_cns = -x ava-ont -t 32 -k 21 -w 21