Date:
10/02/09 07:44
|
Submitted by:
gawbul
|
Assigned to:
unset
|
Category:
Clustering
|
Priority:
5
|
Ticket group:
Critical
|
Resolution:
Unset
|
Summary:
CD-HIT Segmentation fault whilst writing new database
|
Original submission:
hostname:cd-hit user$ sudo ~/Downloads/cd-hit/cd-hit -i out.fas -o cdhitout.fas
total seq: 88
longest and shortest : 1776 and 293
Total letters: 101079
Sequences have been sorted
88 finished 4 clusters
writing new database
Segmentation fault
|
|
Please log in to add comments and receive followups via email.
|
|
Followups
|
Comment
|
Date
|
By
|
Same here on amd64.
In the db_read_and_write function in cd-hi-class.c++,
char buffer1[MAX_LINE_SIZE];
needs to be changed to:
char *buffer1 = (char *) malloc(sizeof(char) * MAX_LINE_SIZE);
(This just makes the suggestion of soulcheck explicit)
|
01/07/10 04:50
|
micha
|
Same happens to me on amd64 linux machines. I narrowed it down to db_read_and_write function in cd-hi-class.c++.
The problem is caused by not enough stack space for buffer1 array. Changing it to be allocated on the heap solves the problem.
Can be resolved as well by increasing stack size with
ulimit -s <new-stack-size>
|
11/03/09 04:59
|
soulcheck
|
|
|
No results for "Dependent on ticket"
|
No results for "Dependent on Task"
|
|
No other tickets are dependent on this ticket
|
|
Ticket change history
|
Field
|
Old value
|
Date
|
By
|
|
status_id
|
Pending |
07/14/11 01:23
|
liwz
|
|
close_date
|
12/31/69 19:00 |
07/14/11 01:23
|
liwz
|
|
![[University of Birmingham]](https://www.bioinformatics.org/images/ack_banners/Birmingham-728x90.gif)
![[Patsnap]](https://www.bioinformatics.org/images/ack_banners/Patsnap-728x90.png)
![[?]](https://www.bioinformatics.org/images/icons/info.png){kind=icon}
