Segmentation fault (core dumped) #augustus
0
0
Entering edit mode
5.1 years ago
ashaneev07 ▴ 40

Hiii...augustus has stopped working by showing the following error. How do I fix this? .Please help me to solve this.Thankyou..

Segmentation fault      (core dumped) augustus --gff3=on --species=maize  PRN01.scaffolds.fa > PRN01.augstus.gff3
assembly augustus software gene prediction • 2.4k views
ADD COMMENT
1
Entering edit mode

this usually points to lack of memory for running the job.

Can you give us an idea of the specs of the machine/server you are running this on? (or of the job parameters if it is running on a cluster)?

ADD REPLY
0
Entering edit mode

sure. Using PC with following specifications. memory 16 gb Os type 64 bit disk space 2 tb

ADD REPLY
0
Entering edit mode

hmm, 16Gb mem might be too low I think (especially for maize)

any idea about the mem-usage of this commandline?

Do you have access to a higher mem machine? if so, try to run it over there with more mem

ADD REPLY
0
Entering edit mode

free -m command shows lyk dis..

              total        used        free      shared  buff/cache   available
Mem:          15952        3184        3735         733        9033       11706
Swap:          2047           0        2047
ADD REPLY
0
Entering edit mode

You may consider monitoring the memory usage of the program via top (or other methods) to see how much memory it's using while actually running.

ADD REPLY
0
Entering edit mode

Here is the outcome of top

top - 12:47:49 up 24 days, 23:55,  1 user,  load average: 0.54, 0.56, 0.68
Tasks: 292 total,   2 running, 237 sleeping,   0 stopped,   0 zombie
%Cpu(s): 25.2 us,  0.4 sy,  0.0 ni, 74.1 id,  0.0 wa,  0.0 hi,  0.2 si,  0.0 st
KiB Mem : 16335736 total,   951532 free,  3570792 used, 11813412 buff/cache
KiB Swap:  2097148 total,  2097148 free,        0 used. 11533148 avail Mem 

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                   
 8256 dcb       20   0  167956 144912   5676 R  99.7  0.9   0:19.10 augustus                                                                  
30616 root      20   0       0      0      0 I   1.3  0.0   0:00.89 kworker/u8:1-i9                                                           
  874 root      20   0  772968  15372  11488 S   0.3  0.1   3:07.47 NetworkManager                                                            
 1491 dcb       20   0 4039588 457244  77564 S   0.3  2.8  68:14.60 gnome-shell                                                               
 1642 dcb       20   0  675104  29636  18388 S   0.3  0.2  27:36.62 gsd-color                                                                 
 2111 dcb       20   0  810840  45688  26828 S   0.3  0.3  47:04.89 gnome-terminal-                                                           
 8216 root      20   0       0      0      0 I   0.3  0.0   0:00.22 kworker/u8:2-cf                                                           
 8262 dcb       20   0   51316   4136   3336 R   0.3  0.0   0:00.03 top
ADD REPLY
0
Entering edit mode

Is this solved or do you need further assistance?

ADD REPLY

Login before adding your answer.

Traffic: 2563 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6