NextDenovo seems not working properly...

[Zuoying Xiahou]

Question or Expected behavior
NextDenovo seems to have stopped working

Operating system
Which operating system and version are you using?
Linux version 3.10.0-514.el7.x86_64 ([e-mail]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC) ) #1 SMP Tue Nov 22 16:42:41 UTC 2016

GCC
What version of GCC are you using?
gcc version 7.2.0 (GCC)

Python
What version of Python are you using?
Python 3.9.5

NextDenovo
What version of NextDenovo are you using?
nextDenovo v2.5.0

Additional context (Optional)
After the first stat job, it seems to stop running, there were no more files update, but the state of the job shows still running. I am not sure if it is a problem...
The file of nextDenovo.sh.done is empty. The run.cfg file's code as follows:

[General]
job_type = lsf
job_prefix = nextDenovo
task = assemble # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 4
input_type = corrected
read_type = clr
input_fofn = ./input.fofn
workdir = nextdenovo_rundir

[correct_option]
read_cutoff = 1k
genome_size = 1700000000
pa_correction = 4
sort_options = -m 64g -t 8
minimap2_options_raw =  -t 8
correction_options = -p 8

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

The nextdenovo_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e shows as follow:

hostname
+ hostname
cd /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/nextdenovo_rundir/01.raw_align/01.db_stat.sh.work/db_stat1
+ cd /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/nextdenovo_rundir/01.raw_align/01.db_stat.sh.work/db_stat1
/ds3200_1/users_root/xiahouzuoying/software/NextDenovo/bin/seq_stat -f 1k -g 1700000000 -d 45 -o /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/nextdenovo_rundir/01.raw_align/input.reads.stat /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/input.fofn
+ /ds3200_1/users_root/xiahouzuoying/software/NextDenovo/bin/seq_stat -f 1k -g 1700000000 -d 45 -o /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/nextdenovo_rundir/01.raw_align/input.reads.stat /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/input.fofn
touch /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/nextdenovo_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.done
+ touch /ds3200_1/users_root/xiahouzuoying/workspace/work_cyc_nextdenovo/nextdenovo_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.done

[Zuoying Xiahou]

Nothing new since 3pm yesterday, but it keeps showing it's running...

[Hu Jiang]

Have you run the test data successfully?

[Zuoying Xiahou]

Have you run the test data successfully?

Yes, I've run the test data. Successfully.

[Hu Jiang]

with job_type = lsf ? if not, have a try.

[Zuoying Xiahou]

with job_type = lsf ? if not, have a try.
I just run the test data with job_type = lsf , the same problem arose.

[Hu Jiang]

Could you paste the output of the tree command in the working directory?

[Zuoying Xiahou]

.
├── 01.raw_align
│   ├── 01.db_stat.sh
│   ├── 01.db_stat.sh.work
│   │   └── db_stat1
│   │   ├── nextDenovo.sh
│   │   ├── nextDenovo.sh.done
│   │   ├── nextDenovo.sh.e
│   │   └── nextDenovo.sh.o
│   └── input.reads.stat
├── 02.cns_align
└── 03.ctg_graph

5 directories, 6 files

[Hu Jiang]

Could you try this testing, it seems this bug caused by ParallelTask

[Zuoying Xiahou]

Hi,
I've tried this testing, but the finally output file is empty.