Segmentation fault, cuffdiff

labrat73 · 11-09-2010, 08:35 AM

Greetings,

I am trying to run cuffdiff and at each attempt am met with the message "Segmentation fault".

I have seen at least two posts from users who encountered the same message, but have not seen any replies addressing this problem.

I would greatly appreciate any assistance.

Many thanks!

nimmi · 11-30-2010, 11:45 AM

I am also encountering the same problem. It would be great if someone can suggest a solution to this.

Thanks in advance.

adarob · 11-30-2010, 12:18 PM

At what point in the process does the fault occur? What is the output that surrounds it?

Please PM me if you have a (preferably small) dataset that exhibits this issue and you're willing to upload it for me to recreate the error.

nimmi · 11-30-2010, 12:32 PM

Hi,
Thank you for your response.

Here is the command that I am using:

cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

Each *.sam file is ~50G so not sure if I can upload them.

Best Regards
Nirmala

adarob · 11-30-2010, 03:48 PM

Where in the process is it when it crashes?

nimmi · 11-30-2010, 07:30 PM

It stops immediately giving a segmentation fault error

pbseq · 12-01-2010, 07:55 AM

in cuffdiff, the -o option should be followed by the results output directory, not by the transcript gtf file. try deleting -o in your command:
cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

nimmi · 12-01-2010, 09:15 AM

Sorry it was a typo in my previous post. Here's the command:

cuffdiff -o cuffDiffOutput ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

gzhao · 04-18-2011, 09:59 AM

I just find out that the output directory must not already exist when you run the cuffdiff command. If it's already there cuffdiff will give segmentation fault. cuffdiff will create it.

lshen · 05-17-2011, 08:45 PM

Quote:

Originally Posted by gzhao

I just find out that the output directory must not already exist when you run the cuffdiff command. If it's already there cuffdiff will give segmentation fault. cuffdiff will create it.

You are right. I got same issue in version v1.0.1 after I run cuffmerge, but at first I thought it is some issue with the merged tanscripts.gtf.

lshen · 05-18-2011, 03:32 AM

If the folder name for -o i cuffdiff is long, I also got same error message. I used a shorter name worked fine.

kaus · 12-17-2014, 01:59 PM

I'm using cuffdiff for the first time and got the segmentation fault error. Someone suggested it might be a memory issue but I'm using a MacPro 16G RAM and 8 cores so I don't think that's it. As for the output file thing as suggested by gzhao and Ishen, I removed that option altogether (as well as all other options) so output should be in the default directory. Still doesn't work. I've tried using both Cufflinks 2.2.0 and 2.2.1.
Any help will be greatly appreciated.

dog941013 · 03-22-2018, 12:00 PM

I got the same problem but it turns out I didn't include the label option. Maybe you can try with the -L commend

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
soapsnp segmentation fault - help!	jtjli	Bioinformatics	6	02-29-2016 09:54 AM
Segmentation fault in sift4.03	nkwuji	Bioinformatics	2	12-20-2011 11:35 PM
cufflinks segmentation fault help please	seq_newbie	Bioinformatics	1	06-29-2011 12:52 PM
SOAP:segmentation fault	Mansequencer	Bioinformatics	1	11-19-2010 11:47 AM
see segmentation fault in soapsnp	guoweiguowei@gmail.com	Bioinformatics	3	04-21-2010 10:15 PM

11-09-2010, 08:35 AM	#1
labrat73 Member Location: Louisiana Join Date: Nov 2010 Posts: 12	Segmentation fault, cuffdiff Greetings, I am trying to run cuffdiff and at each attempt am met with the message "Segmentation fault". I have seen at least two posts from users who encountered the same message, but have not seen any replies addressing this problem. I would greatly appreciate any assistance. Many thanks!

04-18-2011, 09:59 AM	#9
gzhao Junior Member Location: st. Louis Join Date: Apr 2011 Posts: 1	I just find out that the output directory must not already exist when you run the cuffdiff command. If it's already there cuffdiff will give segmentation fault. cuffdiff will create it. Last edited by gzhao; 04-18-2011 at 10:02 AM.

12-17-2014, 01:59 PM	#12
kaus Junior Member Location: NY Join Date: Dec 2014 Posts: 2	same problem - can't fix I'm using cuffdiff for the first time and got the segmentation fault error. Someone suggested it might be a memory issue but I'm using a MacPro 16G RAM and 8 cores so I don't think that's it. As for the output file thing as suggested by gzhao and Ishen, I removed that option altogether (as well as all other options) so output should be in the default directory. Still doesn't work. I've tried using both Cufflinks 2.2.0 and 2.2.1. Any help will be greatly appreciated.

11-30-2010, 11:45 AM	#2
nimmi Member Location: Bethesda Join Date: Jul 2010 Posts: 15	I am also encountering the same problem. It would be great if someone can suggest a solution to this. Thanks in advance.

11-30-2010, 12:18 PM	#3
adarob Member Location: Berkeley, CA Join Date: Jul 2010 Posts: 71	At what point in the process does the fault occur? What is the output that surrounds it? Please PM me if you have a (preferably small) dataset that exhibits this issue and you're willing to upload it for me to recreate the error.

11-30-2010, 12:32 PM	#4
nimmi Member Location: Bethesda Join Date: Jul 2010 Posts: 15	Hi, Thank you for your response. Here is the command that I am using: cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam Each *.sam file is ~50G so not sure if I can upload them. Best Regards Nirmala

11-30-2010, 03:48 PM	#5
adarob Member Location: Berkeley, CA Join Date: Jul 2010 Posts: 71	Where in the process is it when it crashes?

11-30-2010, 07:30 PM	#6
nimmi Member Location: Bethesda Join Date: Jul 2010 Posts: 15	It stops immediately giving a segmentation fault error

12-01-2010, 07:55 AM	#7
pbseq Member Location: italy Join Date: Feb 2010 Posts: 16	in cuffdiff, the -o option should be followed by the results output directory, not by the transcript gtf file. try deleting -o in your command: cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

12-01-2010, 09:15 AM	#8
nimmi Member Location: Bethesda Join Date: Jul 2010 Posts: 15	Sorry it was a typo in my previous post. Here's the command: cuffdiff -o cuffDiffOutput ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

05-18-2011, 03:32 AM	#11
lshen Member Location: Toronto Join Date: Jan 2008 Posts: 30	If the folder name for -o i cuffdiff is long, I also got same error message. I used a shorter name worked fine.

03-22-2018, 12:00 PM	#13
dog941013 Junior Member Location: CT Join Date: Mar 2018 Posts: 1	I got the same problem but it turns out I didn't include the label option. Maybe you can try with the -L commend