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Old 11-09-2010, 07:35 AM   #1
labrat73
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Default 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!
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Old 11-30-2010, 10:45 AM   #2
nimmi
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I am also encountering the same problem. It would be great if someone can suggest a solution to this.

Thanks in advance.
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Old 11-30-2010, 11:18 AM   #3
adarob
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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.
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Old 11-30-2010, 11:32 AM   #4
nimmi
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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
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Old 11-30-2010, 02:48 PM   #5
adarob
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Where in the process is it when it crashes?
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Old 11-30-2010, 06:30 PM   #6
nimmi
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It stops immediately giving a segmentation fault error
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Old 12-01-2010, 06:55 AM   #7
pbseq
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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
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Old 12-01-2010, 08:15 AM   #8
nimmi
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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
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Old 04-18-2011, 08:59 AM   #9
gzhao
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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 09:02 AM.
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Old 05-17-2011, 07:45 PM   #10
lshen
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Quote:
Originally Posted by gzhao View Post
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.
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Old 05-18-2011, 02:32 AM   #11
lshen
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If the folder name for -o i cuffdiff is long, I also got same error message. I used a shorter name worked fine.
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Old 12-17-2014, 12:59 PM   #12
kaus
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Default 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.
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Old 03-22-2018, 11:00 AM   #13
dog941013
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I got the same problem but it turns out I didn't include the label option. Maybe you can try with the -L commend
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