Error: '/bin/sh nextdenovo/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align001/nextDenovo.sh

[qianqianqian0717]

Hi, Dr. Hu
I ran into this problem when I assembled the genome from ONT data and couldn't solve it:

Exception: Command '/bin/sh 01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align001/nextDenovo.sh > 01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align001/nextDenovo.sh.o 2> 01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align001/nextDenovo.sh.e' returned non-zero exit status 1, error info: .

My configuration file run.cfg is as follows

[General]
job_type = local
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 6
parallel_jobs = 20
input_type = raw
read_type = ont
input_fofn = input.fofn
workdir = 01_rundir

[correct_option]
read_cutoff = 1k
genome_size = 480M
seed_cutoff = 57862
blocksize = 2g
pa_correction = 15
seed_cutfiles = 20
sort_options = -m 1g -t 10 -k 40
minimap2_options_raw = - x ava-ont -t 8
correction_options = -p 15

[assemble_option]
random_round = 20
minimap2_options_cns = -x ava-ont -t 8 -k17 -w17
nextgraph_options = -a 1

Could you give me some advice?
Thanks

[moold]

Could you paste the content of file 01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align001/nextDenovo.sh.e to here?

[qianqianqian0717]

Hi, Dr. Hu
Here is the file:

hostname

• hostname
  cd 01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align003
• cd 01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/raw_align003
  time NextDenovo/bin/minimap2-nd --step 1 --dual=yes - x ava-ont -t 8 -x ava-ont 01_rundir/01.raw_align/input.seed.008.2bit 01_rundir/01.raw_align/input.part.017.2bit -o input.seed.008.2bit.2.ovl;
• NextDenovo/bin/minimap2-nd --step 1 --dual=yes - x ava-ont -t 8 -x ava-ont 01_rundir/01.raw_align/input.seed.008.2bit 01_rundir/01.raw_align/input.part.017.2bit -o input.seed.008.2bit.2.ovl
  [ERROR] failed to find seq file type or empty file

real 0m0.702s
user 0m0.468s
sys 0m0.211s

[moold]

As the log says, the input files 01_rundir/01.raw_align/input.seed.008.2bit or 01_rundir/01.raw_align/input.part.017.2bit is empty, so pls check your input input_fofn and the log file in 01_rundir/01.raw_align/02.db_split.sh.work/db_split1/nextDenovo.sh.e

[qianqianqian0717]

Hi, Dr. Hu
I have checked my input_fofn file and log file, input_fofn file only contains the path of the ONT data in fastq.gz format, and the error in the log file is the same as above. Beyond that, the input files 01_rundir/01.raw_align/input.seed.008.2bit was also checked and found to be 224M.

[moold]

How about 01_rundir/01.raw_align/input.part.017.2bit ?

[qianqianqian0717]

Its file size is also 224MB

[moold]

Try to reinstall the lastest version of NextDenovo and rerun from the beginning.

[hafizmtalha]

Hi Dr.
M facing the similar error:

command '/bin/sh /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh > /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh.o 2> /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh.e' returned non-zero exit status 137, error info: .
Traceback (most recent call last):
File "./nextDenovo", line 850, in
main(args)
File "./nextDenovo", line 648, in main
task.run.start()
File "/home/navi/.local/lib/python3.8/site-packages/paralleltask/task_control.py", line 344, in start
self._start()
File "/home/navi/.local/lib/python3.8/site-packages/paralleltask/task_control.py", line 368, in _start
self.submit(job)
File "/home/navi/.local/lib/python3.8/site-packages/paralleltask/task_control.py", line 252, in submit
_, stdout, _ = self.run(job.cmd)
File "/home/navi/.local/lib/python3.8/site-packages/paralleltask/task_control.py", line 288, in run
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/usr/lib/python3.8/logging/init.py", line 1493, in critical
self._log(CRITICAL, msg, args, **kwargs)
File "/usr/lib/python3.8/logging/init.py", line 1589, in _log
self.handle(record)
File "/usr/lib/python3.8/logging/init.py", line 1599, in handle
self.callHandlers(record)
File "/usr/lib/python3.8/logging/init.py", line 1661, in callHandlers
hdlr.handle(record)
File "/usr/lib/python3.8/logging/init.py", line 954, in handle
self.emit(record)
File "/home/navi/.local/lib/python3.8/site-packages/paralleltask/kit.py", line 42, in emit
raise Exception(record.msg)
Exception: Command '/bin/sh /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh > /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh.o 2> /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh.e' returned non-zero exit status 137, error info: .

raw_align08/nextDenovo.sh.e files has the following error

hostname

• hostname
  cd /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08
• cd /home/navi/magnaporthe-KI215/assembly_number_3/01.raw_align/03.raw_align.sh.work/raw_align08
  time /home/navi/magnaporthe-KI215/NextDenovo/bin/minimap2-nd --step 1 -I 3G --dual=yes -t 5 -x ava-ont /home/navi/magnaporthe-KI215/NextDenovo/../assembly_number_3/01.raw_align/input.seed.001.2bit /home/navi/magnaporthe-KI215/NextDenovo/../assembly_number_3/01.raw_align/input.seed.003.2bit -o input.seed.001.2bit.4.ovl;ln -sf input.seed.001.2bit.4.ovl input.seed.003.2bit.4.ovl;
• time /home/navi/magnaporthe-KI215/NextDenovo/bin/minimap2-nd --step 1 -I 3G --dual=yes -t 5 -x ava-ont /home/navi/magnaporthe-KI215/NextDenovo/../assembly_number_3/01.raw_align/input.seed.001.2bit /home/navi/magnaporthe-KI215/NextDenovo/../assembly_number_3/01.raw_align/input.seed.003.2bit -o input.seed.001.2bit.4.ovl
  [M::mm_idx_gen::14.3311.71] collected minimizers
  [M::mm_idx_gen::18.6642.03] sorted minimizers
  [M::main::18.6642.03] loaded/built the index for 17850 target sequence(s)
  [M::mm_mapopt_update::19.7471.97] mid_occ = 439
  [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 17850
  [M::mm_idx_stat::20.756*1.90] distinct minimizers: 63051508 (63.44% are singletons); average occurrences: 3.650; average spacing: 2.932
  Command terminated by signal 9
  288.60user 7.99system 1:35.15elapsed 311%CPU (0avgtext+0avgdata 6486324maxresident)k
  488384inputs+24outputs (719major+3395948minor)pagefaults 0swaps

[moold]

It seems you don't have enough memory, try to reduceparallel_jobs and pa_correction