non-zero exit status 137, error info: . - assembly still finishes though
JWDebler opened this issue · comments
Describe the bug
I'm running the latest version 2.5.2.
This might be a strange conda problem.
mamba activate nextdenovo
ubuntu@bifo-server:python --version
Python 3.9.13
ubuntu@bifo-server:which python
/home/ubuntu/mambaforge/envs/nextdenovo/bin/python
ubuntu@bifo-server:/home/ubuntu/mambaforge/envs/nextdenovo/bin/python --version
Python 3.11.3
Somehow python runs 3.9.13, but the full path to it runs 3.11.3
Error message
This python error prints after every instance of the CRITICAL message in the main logfile:
Traceback (most recent call last):
File "/opt/nextdenovo/NextDenovo/nextDenovo", line 857, in <module>
main(args)
File "/opt/nextdenovo/NextDenovo/nextDenovo", line 660, in main
task.run.rerun()
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/site-packages/paralleltask/task_control.py", line 296, in rerun
self.start()
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/site-packages/paralleltask/task_control.py", line 348, in start
self._start()
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/site-packages/paralleltask/task_control.py", line 372, in _start
self.submit(job)
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/site-packages/paralleltask/task_control.py", line 252, in submit
_, stdout, _ = self.run(job.cmd)
^^^^^^^^^^^^^^^^^
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/site-packages/paralleltask/task_control.py", line 292, in run
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/logging/__init__.py", line 1536, in critical
self._log(CRITICAL, msg, args, **kwargs)
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/logging/__init__.py", line 1634, in _log
self.handle(record)
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/logging/__init__.py", line 1644, in handle
self.callHandlers(record)
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/logging/__init__.py", line 1706, in callHandlers
hdlr.handle(record)
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/logging/__init__.py", line 978, in handle
self.emit(record)
File "/home/ubuntu/mambaforge/envs/nextdenovo/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit
raise Exception(record.msg)
Exception: Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh > /data/assembler_comp/
15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh
.work/raw_align08/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
Here's the main logfile, as you can see there are several [CRITICAL] messages, yet the assembly still finishes.
[6452 INFO] 2023-05-23 02:49:04 NextDenovo start...
[6452 INFO] 2023-05-23 02:49:04 version:2.5.2 logfile:pid6452.log.info
[6452 WARNING] 2023-05-23 02:49:04 Re-write workdir
[6452 INFO] 2023-05-23 02:49:04 mkdir: /data/assembler_comp/15CUR005.nextdenovo
[6452 INFO] 2023-05-23 02:49:04 mkdir: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align
[6452 INFO] 2023-05-23 02:49:04 mkdir: /data/assembler_comp/15CUR005.nextdenovo/02.cns_align
[6452 INFO] 2023-05-23 02:49:04 mkdir: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph
[6452 INFO] 2023-05-23 02:49:09 Total jobs: 1
[6452 INFO] 2023-05-23 02:49:09 Submitted jobID:[10859] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/01.db_stat.sh.work/db_stat1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:55:06 db_stat done
[6452 INFO] 2023-05-23 02:55:06 updated options:
rerun: 3
task: all
deltmp: 1
rewrite: 1
read_type: ont
job_type: local
input_type: raw
read_cutoff: 1k
seed_depth: 45.0
pa_correction: 5
seed_cutfiles: 5
genome_size: 42m
parallel_jobs: 10
seed_cutoff: 17194
blocksize: 593679883
ctg_cns_options: -p 30
nextgraph_options: -a 1
job_prefix: 15CUR005.nextdenovo
sort_options: -m 50g -t 30 -k 40
minimap2_options_map: -x map-ont
minimap2_options_raw: -t 8 -x ava-ont
input_fofn: /data/assembler_comp/15CUR005.fofn
workdir: /data/assembler_comp/15CUR005.nextdenovo
raw_aligndir: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align
cns_aligndir: /data/assembler_comp/15CUR005.nextdenovo/02.cns_align
ctg_graphdir: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph
correction_options: -p 30 -max_lq_length 10000 -r ont -min_len_seed 8597
minimap2_options_cns: -t 8 -x ava-ont -k 17 -w 17 --minlen 1719 --maxhan1 5000
[6452 INFO] 2023-05-23 02:55:06 summary of input data:
file:�[35m /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/input.reads.stat �[0m
[Read length stat]
Types Count (#) Length (bp)
N10 7771 38279
N20 18623 30342
N30 31970 25087
N40 47948 21093
N50 66974 17667
N60 89748 14665
N70 117516 11858
N80 152799 9064
N90 201508 6150
Types Count (#) Bases (bp) Depth (X)
Raw 286834 3668039649 87.33
Filtered 0 0 0.00
Clean 286834 3668039649 87.33
*Suggested seed_cutoff (genome size: 42.00Mb, expected seed depth: 45, real seed depth: 45.00): 17194 bp
[6452 INFO] 2023-05-23 02:55:11 Total jobs: 1
[6452 INFO] 2023-05-23 02:55:11 Submitted jobID:[31845] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/02.db_split.sh.work/db_split1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:51 db_split done
[6452 INFO] 2023-05-23 02:56:51 Total jobs: 30
[6452 INFO] 2023-05-23 02:56:51 Submitted jobID:[11936] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align01/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:52 Submitted jobID:[11970] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align02/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:52 Submitted jobID:[12028] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align03/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:53 Submitted jobID:[12084] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align04/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:53 Submitted jobID:[12126] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:54 Submitted jobID:[12135] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align06/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:54 Submitted jobID:[12177] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:55 Submitted jobID:[12352] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:55 Submitted jobID:[12595] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align09/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 02:56:56 Submitted jobID:[12792] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align10/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:10:37 Submitted jobID:[27580] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align11/15CUR005.nextdenovo.sh] in the local_cycle.
[12352 CRITICAL] 2023-05-23 03:12:40 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:12:43 Submitted jobID:[30308] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align12/15CUR005.nextdenovo.sh] in the local_cycle.
[12126 CRITICAL] 2023-05-23 03:14:46 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:14:48 Submitted jobID:[31082] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align13/15CUR005.nextdenovo.sh] in the local_cycle.
[12177 CRITICAL] 2023-05-23 03:16:56 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:16:59 Submitted jobID:[9021] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align14/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:18:14 Submitted jobID:[28382] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align15/15CUR005.nextdenovo.sh] in the local_cycle.
[11970 CRITICAL] 2023-05-23 03:20:32 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align02/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align02/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align02/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:20:34 Submitted jobID:[6297] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align16/15CUR005.nextdenovo.sh] in the local_cycle.
[12028 CRITICAL] 2023-05-23 03:22:55 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align03/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align03/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align03/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:22:57 Submitted jobID:[13186] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align17/15CUR005.nextdenovo.sh] in the local_cycle.
[12792 CRITICAL] 2023-05-23 03:25:01 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align10/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align10/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align10/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:25:05 Submitted jobID:[16054] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align18/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:25:08 Submitted jobID:[18052] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align19/15CUR005.nextdenovo.sh] in the local_cycle.
[12595 CRITICAL] 2023-05-23 03:28:21 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align09/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align09/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align09/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:28:23 Submitted jobID:[27411] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align20/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:31:07 Submitted jobID:[21633] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align21/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:35:29 Submitted jobID:[2729] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align22/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:36:40 Submitted jobID:[26722] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align23/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:37:35 Submitted jobID:[10298] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align24/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:38:22 Submitted jobID:[24558] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align25/15CUR005.nextdenovo.sh] in the local_cycle.
[27580 CRITICAL] 2023-05-23 03:40:40 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align11/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align11/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align11/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:40:42 Submitted jobID:[25886] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align26/15CUR005.nextdenovo.sh] in the local_cycle.
[6297 CRITICAL] 2023-05-23 03:42:53 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align16/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align16/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align16/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:42:54 Submitted jobID:[20102] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align27/15CUR005.nextdenovo.sh] in the local_cycle.
[13186 CRITICAL] 2023-05-23 03:44:43 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align17/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align17/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align17/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 03:44:44 Submitted jobID:[9511] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align28/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:45:10 Submitted jobID:[14953] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align29/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 03:47:44 Submitted jobID:[15292] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align30/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:45 10 raw_align jobs failed, and rerun for the 3 time
[6452 INFO] 2023-05-23 04:10:45 Total jobs: 10
[6452 INFO] 2023-05-23 04:10:45 Submitted jobID:[19402] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align02/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:45 Submitted jobID:[19485] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align03/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:46 Submitted jobID:[19579] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:46 Submitted jobID:[19672] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:47 Submitted jobID:[19688] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:47 Submitted jobID:[19700] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align09/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:48 Submitted jobID:[19706] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align10/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:48 Submitted jobID:[19715] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align11/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:49 Submitted jobID:[19724] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align16/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:10:49 Submitted jobID:[19732] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align17/15CUR005.nextdenovo.sh] in the local_cycle.
[19688 CRITICAL] 2023-05-23 04:22:44 Command '/bin/bash /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh > /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh.o 2> /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh.e' returned non-zero exit status 137, error info: .
[6452 INFO] 2023-05-23 04:33:43 1 raw_align jobs failed, and rerun for the 2 time
[6452 INFO] 2023-05-23 04:33:43 Total jobs: 1
[6452 INFO] 2023-05-23 04:33:43 Submitted jobID:[3808] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:37:21 raw_align done
[6452 INFO] 2023-05-23 04:37:21 Total jobs: 5
[6452 INFO] 2023-05-23 04:37:21 Submitted jobID:[5000] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/04.sort_align.sh.work/sort_align1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:37:21 Submitted jobID:[5006] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/04.sort_align.sh.work/sort_align2/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:37:22 Submitted jobID:[5012] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/04.sort_align.sh.work/sort_align3/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:37:22 Submitted jobID:[5018] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/04.sort_align.sh.work/sort_align4/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:37:23 Submitted jobID:[5038] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/01.raw_align/04.sort_align.sh.work/sort_align5/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:38:44 sort_align done
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/input.seed.003.2bit.4.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align09/input.seed.003.2bit.8.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align10/input.seed.003.2bit.9.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align11/input.seed.003.2bit.10.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align12/input.seed.003.2bit.11.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align13/input.seed.003.2bit.12.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align14/input.seed.003.2bit.13.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align15/input.seed.003.2bit.14.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/input.seed.002.2bit.7.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align15/input.seed.002.2bit.14.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align21/input.seed.002.2bit.20.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align26/input.seed.002.2bit.25.ovl
[6452 INFO] 2023-05-23 04:38:44 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align27/input.seed.002.2bit.26.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align28/input.seed.002.2bit.27.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align29/input.seed.002.2bit.28.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align30/input.seed.002.2bit.29.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/input.seed.004.2bit.6.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align14/input.seed.004.2bit.13.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align20/input.seed.004.2bit.19.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align22/input.seed.004.2bit.21.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align23/input.seed.004.2bit.22.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align24/input.seed.004.2bit.23.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align25/input.seed.004.2bit.24.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align26/input.seed.004.2bit.25.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align01/input.seed.005.2bit.0.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align02/input.seed.005.2bit.1.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align03/input.seed.005.2bit.2.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align04/input.seed.005.2bit.3.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align05/input.seed.005.2bit.4.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align06/input.seed.005.2bit.5.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align07/input.seed.005.2bit.6.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align08/input.seed.005.2bit.7.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align06/input.seed.001.2bit.5.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align13/input.seed.001.2bit.12.ovl
[6452 INFO] 2023-05-23 04:38:45 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align16/input.seed.001.2bit.15.ovl
[6452 INFO] 2023-05-23 04:38:46 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align17/input.seed.001.2bit.16.ovl
[6452 INFO] 2023-05-23 04:38:46 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align18/input.seed.001.2bit.17.ovl
[6452 INFO] 2023-05-23 04:38:46 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align19/input.seed.001.2bit.18.ovl
[6452 INFO] 2023-05-23 04:38:46 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align20/input.seed.001.2bit.19.ovl
[6452 INFO] 2023-05-23 04:38:46 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align21/input.seed.001.2bit.20.ovl
[6452 INFO] 2023-05-23 04:38:46 Total jobs: 5
[6452 INFO] 2023-05-23 04:38:46 Submitted jobID:[7936] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/01.seed_cns.sh.work/seed_cns1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:38:46 Submitted jobID:[7944] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/01.seed_cns.sh.work/seed_cns2/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:38:47 Submitted jobID:[7950] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/01.seed_cns.sh.work/seed_cns3/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:38:47 Submitted jobID:[7960] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/01.seed_cns.sh.work/seed_cns4/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:38:48 Submitted jobID:[8054] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/01.seed_cns.sh.work/seed_cns5/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:42:58 seed_cns done
[6452 INFO] 2023-05-23 04:42:58 seed_cns finished, and final corrected reads file:
[6452 INFO] 2023-05-23 04:42:58 �[35m /data/assembler_comp/15CUR005.nextdenovo/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta �[0m
[6452 INFO] 2023-05-23 04:42:58 Total jobs: 15
[6452 INFO] 2023-05-23 04:42:58 Submitted jobID:[16890] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align01/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:42:58 Submitted jobID:[16898] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align02/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:42:59 Submitted jobID:[16904] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align03/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:42:59 Submitted jobID:[16910] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align04/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:43:00 Submitted jobID:[16922] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align05/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:43:00 Submitted jobID:[16928] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align06/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:43:01 Submitted jobID:[16975] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align07/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:43:01 Submitted jobID:[17070] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align08/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:43:02 Submitted jobID:[17118] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align09/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 04:43:02 Submitted jobID:[17124] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align10/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:04:25 Submitted jobID:[24109] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align11/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:08:29 Submitted jobID:[30799] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align12/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:15:49 Submitted jobID:[10386] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align13/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:16:37 Submitted jobID:[11693] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align14/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:24:26 Submitted jobID:[14272] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/02.cns_align/02.cns_align.sh.work/cns_align15/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:35:40 cns_align done
[6452 INFO] 2023-05-23 05:35:45 Total jobs: 1
[6452 INFO] 2023-05-23 05:35:45 Submitted jobID:[18177] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:35:47 ctg_graph done
[6452 INFO] 2023-05-23 05:35:47 Total jobs: 5
[6452 INFO] 2023-05-23 05:35:47 Submitted jobID:[18186] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:35:47 Submitted jobID:[18196] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align2/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:35:48 Submitted jobID:[18206] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:35:48 Submitted jobID:[18246] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align4/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:35:49 Submitted jobID:[18256] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align5/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:37:37 ctg_align done
[6452 INFO] 2023-05-23 05:37:37 Total jobs: 5
[6452 INFO] 2023-05-23 05:37:37 Submitted jobID:[19528] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns1/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:37:37 Submitted jobID:[19545] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns2/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:37:38 Submitted jobID:[19562] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns3/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:37:38 Submitted jobID:[19578] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns4/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:37:39 Submitted jobID:[19598] jobCmd:[/data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns5/15CUR005.nextdenovo.sh] in the local_cycle.
[6452 INFO] 2023-05-23 05:37:57 ctg_cns done
[6452 INFO] 2023-05-23 05:37:57 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align1/input.seed.005.2bit.sort.bam
[6452 INFO] 2023-05-23 05:37:57 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align2/input.seed.003.2bit.sort.bam
[6452 INFO] 2023-05-23 05:37:58 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/input.seed.001.2bit.sort.bam
[6452 INFO] 2023-05-23 05:37:58 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align4/input.seed.004.2bit.sort.bam
[6452 INFO] 2023-05-23 05:37:58 remove temporary result: /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/02.ctg_align.sh.work/ctg_align5/input.seed.002.2bit.sort.bam
[6452 INFO] 2023-05-23 05:37:58 nextDenovo finished
[6452 INFO] 2023-05-23 05:37:58 final assembly file:
[6452 INFO] 2023-05-23 05:37:58 �[35m /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/nd.asm.fasta �[0m
[6452 INFO] 2023-05-23 05:37:58 final stat file:
[6452 INFO] 2023-05-23 05:37:58 �[35m /data/assembler_comp/15CUR005.nextdenovo/03.ctg_graph/nd.asm.fasta.stat �[0m
[6452 INFO] 2023-05-23 05:37:58 asm stat:
[6452 INFO] 2023-05-23 05:37:58
Type Length (bp) Count (#)
N10 2834257 2
N20 2583852 3
N30 2397411 5
N40 1944000 7
N50 1718957 9
N60 1535929 11
N70 1450754 14
N80 1272956 17
N90 1153192 21
Min. 41033 -
Max. 3375119 -
Ave. 1457073 -
Total 40798045 28
Genome characteristics
42 mb homozygous fungal genome
Input data
Q20 Nanopore raw data, filtered to remove <1000 bp reads and keeping only the 90% best reads (filtlong). 286,834 reads, 3,668,039,649 bases
Config file
PROJECT=15CUR005.necat
ONT_READ_LIST=15CUR005.necat.readlist.txt
GENOME_SIZE=42m
THREADS=10
MIN_READ_LENGTH=3000
PREP_OUTPUT_COVERAGE=40
OVLP_FAST_OPTIONS=-n 500 -z 20 -b 2000 -e 0.5 -j 0 -u 1 -a 1000
OVLP_SENSITIVE_OPTIONS=-n 500 -z 10 -e 0.5 -j 0 -u 1 -a 1000
CNS_FAST_OPTIONS=-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0
CNS_SENSITIVE_OPTIONS=-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0
TRIM_OVLP_OPTIONS=-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 1 -a 400
ASM_OVLP_OPTIONS=-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400
NUM_ITER=2
CNS_OUTPUT_COVERAGE=30
CLEANUP=1
USE_GRID=false
GRID_NODE=0
GRID_OPTIONS=
SMALL_MEMORY=0
FSA_OL_FILTER_OPTIONS=
FSA_ASSEMBLE_OPTIONS=
FSA_CTG_BRIDGE_OPTIONS=
POLISH_CONTIGS=true
Operating system
Ubuntu 18.04.6 LTS
GCC
gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
Python
Python 3.9.13 / 3.11.3 (not sure which is used)
NextDenovo
nextDenovo 2.5.2
Looks like the problem was that I was running our of RAM. I played with the config settings a little adjusting the number of parallel tasks and now it seems fine. Cheers.
can you help me to solve this problem？thank you very much！
run.cfg：[General]
job_type = local # local, slurm, sge, pbs, lsf
job_prefix = nextDenovo
task = all # all, correct, assemble
rewrite = yes # yes/no
rerun = 3
deltmp = yes
parallel_jobs = 15 # number of tasks used to run in parallel
input_type = raw # raw, corrected
read_type = ont # clr, ont, hifi
input_fofn = ./input.fofn
workdir = ./01_rundir
[correct_option]
read_cutoff = 1k
seed_cutoff = 23576
genome_size = 487.15m # estimated genome size
sort_options = -m 20g -t 15
minimap2_options_raw = -x ava-ont -t 10
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 -dbuf
[assemble_option]
minimap2_options_cns = -x ava-ont -t 8 -k 17 -w 17
nextgraph_options = -a 1
my Linux RAM
total 128672
used 64326
free 25876
shared 23027
buff/cache 38469
available 40090
[460027 CRITICAL] 2024-06-20 01:55:44 Command '/bin/bash /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh > /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh.o 2> /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh.e' returned non-zero exit status 137, error info: .
Traceback (most recent call last):
File "/data5/fulongwen/opt/biosoft/NextDenovo/nextDenovo", line 857, in
main(args)
File "/data5/fulongwen/opt/biosoft/NextDenovo/nextDenovo", line 651, in main
task.run.start()
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 350, in start
self._start()
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 374, in _start
self.submit(job)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 254, in submit
_, stdout, _ = self.run(job.cmd)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 294, in run
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1219, in critical
self._log(CRITICAL, msg, args, **kwargs)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1293, in _log
self.handle(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1303, in handle
self.callHandlers(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1343, in callHandlers
hdlr.handle(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 766, in handle
self.emit(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/kit.py", line 42, in emit
raise Exception(record.msg)
Exception: Command '/bin/bash /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh > /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh.o 2> /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh.e' returned non-zero exit status 137, error info: .
[460154 CRITICAL] 2024-06-20 01:55:46 Command '/bin/bash /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align11/nextDenovo.sh > /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align11/nextDenovo.sh.o 2> /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align11/nextDenovo.sh.e' returned non-zero exit status 137, error info: .
Traceback (most recent call last):
File "/data5/fulongwen/opt/biosoft/NextDenovo/nextDenovo", line 857, in
main(args)
File "/data5/fulongwen/opt/biosoft/NextDenovo/nextDenovo", line 651, in main
task.run.start()
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 350, in start
self._start()
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 374, in _start
self.submit(job)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 254, in submit
_, stdout, _ = self.run(job.cmd)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/task_control.py", line 294, in run
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1219, in critical
self._log(CRITICAL, msg, args, **kwargs)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1293, in _log
self.handle(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1303, in handle
self.callHandlers(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 1343, in callHandlers
hdlr.handle(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/logging/init.py", line 766, in handle
self.emit(record)
File "/data5/fulongwen/anaconda3/envs/python2.7/lib/python2.7/site-packages/paralleltask/kit.py", line 42, in emit
raise Exception(record.msg)
Exception: Command '/bin/bash /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align11/nextDenovo.sh > /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align11/nextDenovo.sh.o 2> /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align11/nextDenovo.sh.e' returned non-zero exit status 137, error info:
Running our of RAM, so just reduce the value of parallel_jobs and rerun.
Running our of RAM, so just reduce the value of
parallel_jobsand rerun.
I lowered the value of the parallel_jobs to 5 and I still have the same problem
nextDenovo.sh.e is
hostname
- hostname
cd /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align04 - cd /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align04
( time /data5/fulongwen/opt/biosoft/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -x ava-ont -t 10 /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/./01_rundir/01.raw_align/input.seed.003.2bit /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/./01_rundir/01.raw_align/input.part.004.2bit -o input.seed.003.2bit.3.ovl; ) - /data5/fulongwen/opt/biosoft/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -x ava-ont -t 10 /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/./01_rundir/01.raw_align/input.seed.003.2bit /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/./01_rundir/01.raw_align/input.part.004.2bit -o input.seed.003.2bit.3.ovl
/data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align04/nextDenovo.sh: line 5: 548310 Killed /data5/fulongwen/opt/biosoft/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -x ava-ont -t 10 /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/./01_rundir/01.raw_align/input.seed.003.2bit /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/./01_rundir/01.raw_align/input.part.004.2bit -o input.seed.003.2bit.3.ovl
real 0m51.342s
user 0m59.960s
sys 0m22.921s
You can run these failed tasks manually using command: sh nextDenovo.sh After you manually run all failed tasks, you can continue to run the main task. if this doesn't work, you need change a computer with more RAM.