A problem I met when running NextDenovo

[nextomics]

A problem I met when running NextDenovo

[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