Error: db_stat failed ?

[carla-hazelf]

Describe the bug
Hi,
I am submitting ./nextDenovo run.cfg and after 35 mins of run time I get this error. I check the .log but not sure how to interpret what went wrong. I am submitting the job with 450G and 128CPUS per task. Any thoughts?

Error message

> [631262 INFO] 2023-11-03 12:35:35 NextDenovo start...
> [631262 INFO] 2023-11-03 12:35:35 version:2.5.2 logfile:pid631262.log.info
> [631262 WARNING] 2023-11-03 12:35:35 Re-write workdir
> [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir
> [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align
> [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/02.cns_align
> [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/03.ctg_graph
> [631262 INFO] 2023-11-03 12:35:40 Total jobs: 1
> [631262 INFO] 2023-11-03 12:35:40 Submitted jobID:[301031] jobCmd: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the slurm_cycle.
> [631262 ERROR] 2023-11-03 13:33:24 db_stat failed: please check the following logs:
> [631262 ERROR] 2023-11-03 13:33:24 /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e

When I check the nextDenovo.sh.e, I find this:

hostname
+ hostname
cd /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1
+ cd /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1
( time  /ont/assemblies/nextdenovo/NextDenovo/bin/seq_stat -f 1k -g 650m -d 45 -o /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/input.reads.stat /ont/assemblies/nextdenovo/NextDenovo/input.fofn )
+ /ont/assemblies/nextdenovo/NextDenovo/bin/seq_stat -f 1k -g 650m -d 45 -o /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/input.reads.stat /ont/assemblies/nextdenovo/NextDenovo/input.fofn

real	57m1.747s
user	2m17.870s
sys	2m11.257s
touch /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.done
+ touch /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.done

Genome characteristics
Genome size is expected to be ~650Mb.

Input data
ONT .fastq file. Total base count: 86,626,065,745 , sequencing depth x133.27, n50 length 13,995

Config file

[General]
job_type = slurm # local, slurm, sge, pbs, lsf
job_prefix = nextDenovo
task = all # all, correct, assemble
rewrite = yes # yes/no
deltmp = yes 
parallel_jobs = 20 # number of tasks used to run in parallel
input_type = raw # raw, corrected
read_type = ont # clr, ont, hifi
input_fofn = input.fofn
workdir = 02_rundir

[correct_option]
read_cutoff = 1k
genome_size = 650m # estimated genome size
sort_options = -m 20g -t 30
minimap2_options_raw = -x ava-ont -t 32
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 15

[assemble_option]
minimap2_options_cns = -x ava-ont -t 32 -k 21 -w 21
nextgraph_options = -a 1

Operating system
Which operating system and version are you using?

NAME="Rocky Linux"
VERSION="8.8 (Green Obsidian)"

GCC
GCCcore/11.3.0

Python
Python/3.10.4

NextDenovo
2.5.2

[Hu Jiang]

It seems everything is ok, so just rerun the main task.