[Next-Generation Sequencing Book]

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[ Ticket #1103 ] CD-HIT Segmentation fault whilst writing new database
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
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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
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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

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