Segmentation fault (core dumped) #augustus

Question

[ashaneev07]

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

[lieven.sterck]

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)?

[ashaneev07]

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

[lieven.sterck]

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

[ashaneev07]

free -m command shows lyk dis..

              total        used        free      shared  buff/cache   available
Mem:          15952        3184        3735         733        9033       11706
Swap:          2047           0        2047

[jared.andrews07]

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.

[ashaneev07]

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

[ATpoint]

Is this solved or do you need further assistance?