A problem I met when running NextDenovo

[zjwang0831]

Hi! I ran the test example(the command is nohup nextDenovo test/run.cfg & ) Here is run.cfg file:

[General]
job_type = local
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 2
input_type = raw
input_fofn = ./input.fofn
workdir = ./01_rundir

[correct_option]
read_cutoff = 1k
seed_cutoff = 32k
blocksize = 1g
pa_correction = 2
seed_cutfiles = 2
sort_options = -m 1g -t 2 -k 50
minimap2_options_raw = -x ava-ont -t 8
correction_options = -p 15

[assemble_option]
random_round = 10
minimap2_options_cns = -x ava-ont -t 8 -k17 -w17
nextgraph_options = -a 1

But I got error like this:

[INFO] 2019-10-21 17:04:16,871 start...
[INFO] 2019-10-21 17:04:16,871 logfile: pid111095.log.info
[WARNING] 2019-10-21 17:04:16,872 Re-write workdir
[INFO] 2019-10-21 17:04:16,872 options: 
[INFO] 2019-10-21 17:04:16,873 {'sort_threads': 2, 'nodelist': '', 'rewrite': 1, 'blocksize': '1g', 'job_prefix': 'nextDenovo', 'job_type': 'local', 'minimap2_options_raw': '-x ava-ont -t 8', 'cns_threads': 15, 'sort_mem': '1g', 'seed_cutoff': '32000', 'input_fofn': '/h
[INFO] 2019-10-21 17:04:16,873 skip mkdir: /home/lailab/wangzijian/software/NextDenovo/test_data/./01_rundir
[INFO] 2019-10-21 17:04:16,873 skip mkdir: /home/lailab/wangzijian/software/NextDenovo/test_data/./01_rundir/01.raw_align
[INFO] 2019-10-21 17:04:16,873 skip mkdir: /home/lailab/wangzijian/software/NextDenovo/test_data/./01_rundir/02.cns_align
[INFO] 2019-10-21 17:04:16,873 skip mkdir: /home/lailab/wangzijian/software/NextDenovo/test_data/./01_rundir/03.ctg_graph
[INFO] 2019-10-21 17:04:16,874 analysis tasks done
[INFO] 2019-10-21 17:04:16,874 total jobs: 1
[INFO] 2019-10-21 17:04:16,876 Throw jobID:[111096] jobCmd:[/home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh] in the local_cycle.
[ERROR] 2019-10-21 17:04:17,400 db_split failed: please check the following logs:
[ERROR] 2019-10-21 17:04:17,400 /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh.e

Then I checked /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh.e to find out what is the error , which is shown below:

hostname
+ hostname
cd /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0
+ cd /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0
time /home/lailab/wangzijian/software/NextDenovo/bin/seq_dump -f 1k -s 32000 -b 1g -n 2 -d /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align /home/lailab/wangzijian/software/NextDenovo/test_data/input.fofn
+ time /home/lailab/wangzijian/software/NextDenovo/bin/seq_dump -f 1k -s 32000 -b 1g -n 2 -d /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align /home/lailab/wangzijian/software/NextDenovo/test_data/input.fofn
/home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh: 5: /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh: time: not found 

Could you tell me how to deal with it? Thanks a lot!

[moold]

Could you try to run the command time or /usr/bin/time ?

[zjwang0831]

I tried which time,timeand /usr/bin/time . There is a time somewhere but it seems that the system doesn't know where it is, neither do I.

(py27) lailab@debian-07:~/wangzijian/software/NextDenovo$ which time
(py27) lailab@debian-07:~/wangzijian/software/NextDenovo$ time ls
README.md  bin  doc  lib  minimap2  nextDenovo  nohup.out  pid109778.log.info  pid111095.log.info  test_data

real    0m0.002s
user    0m0.000s
sys 0m0.000s
(py27) lailab@debian-07:~/wangzijian/software/NextDenovo$ /usr/bin/time ls
-bash: /usr/bin/time: No such file or directory

[moold]

It seems your system already includes the time command? so could you try to run command time /home/lailab/wangzijian/software/NextDenovo/bin/seq_dump -f 1k -s 32000 -b 1g -n 2 -d /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align /home/lailab/wangzijian/software/NextDenovo/test_data/input.fofn manually?

[zjwang0831]

The system found time when I ran time directly, while the system cannot when I ran in the background.

(py27) lailab@debian-07:~/wangzijian/software/NextDenovo$ nohup time /home/lailab/wangzijian/software/NextDenovo/bin/seq_dump -f 1k -s 32000 -b 1g -n 2 -d /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align /home/lailab/wangzijian/software/NextDenovo/test_data/input.fofn  &
[1] 74494
(py27) lailab@debian-07:~/wangzijian/software/NextDenovo$ nohup: ignoring input and appending output to 'nohup.out'
nohup: failed to run command 'time': No such file or directory

[1]+  Exit 127                nohup time /home/lailab/wangzijian/software/NextDenovo/bin/seq_dump -f 1k -s 32000 -b 1g -n 2 -d /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align /home/lailab/wangzijian/software/NextDenovo/test_data/input.fofn

(py27) lailab@debian-07:~/wangzijian/software/NextDenovo$ time /home/lailab/wangzijian/software/NextDenovo/bin/seq_dump -f 1k -s 32000 -b 1g -n 2 -d /home/lailab/wangzijian/software/NextDenovo/test_data/01_rundir/01.raw_align /home/lailab/wangzijian/software/NextDenovo/test_data/input.fofn

real    0m0.091s
user    0m0.080s
sys 0m0.012s

[moold]

Hi, if you still have this problem, I have an alternative unfriendly method you can try. Change line 138 subtask += 'time ' + task + '\n' in file lib/task_control.py to subtask += task + '\n', It maybe work.

[zjwang0831]

I login the server as root, and install a time , it works know. Thanks for helping!

[moold]

ok