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YeoLab / clipper

A tool to identify CLIP-seq peaks
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'Segmentation fault' issue #88

Open dahun73 opened 3 years ago

dahun73 commented 3 years ago

Hello!

I re-installed clipper but error message came out. image

I used 'conda env create -f environment3.yml'. I tried to fix it but it didn't work. Is there anyone same problem like me?

Thanks! Dahun

ELMMA-FUNNY commented 2 years ago

Hello!

I had the same problem,and I browsed all the issues without finding any methods to slove it. Could you help me?Thanks.@algaebrown

shaojunyu commented 1 year ago

Hi This problem also occurred after I installed the latest code from Github. I'm not sure how to resolve it. It appears to be related to peak.so in the src folder.

image
caggtaagtat commented 1 year ago

I run into the same problem.

Shashankti commented 1 year ago

Hey, I am having the same issue right now. I even tried to install an older version of clipper but that too gave me the same error, wondering if anyone has come up with a solution.

clipper -h
[1]    35719 segmentation fault (core dumped)  clipper -h
PinpinSui commented 1 year ago

Hi,

Does any one have solved the bug Segmentation fault (core dumped) shown when run clipper? Thank you,

Pinpin

antczakp commented 1 year ago

Hi, got the same issue. New install on Ubuntu 22.04 and using the environment causes clipper to segmentation fault - does anybody have a solution for that? Or some idea what to change, we have so far tried to change the gcc version to 8.x, tried several packages higher and lower of the proposed versions yet still we get to a point where clipper just faults without much additional information. Any help would be amazing.

JohnRachid commented 1 year ago

Same issue. Repo seems dead.

cparsania commented 1 year ago

same issue

algaebrown commented 1 year ago

Hi! Sorry for the delay. It can be related to the C extensions. Please make use of this docker image: https://hub.docker.com/r/brianyee/clipper On Apr 25, 2023, 8:47 PM -0700, Chirag Parsania, Ph.D. @.***>, wrote:

same issue — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

cparsania commented 1 year ago

Hi thanks for your reply.

After pulling the image, I tried to run clipper interactively. However, it didn't work. Any idea what's wrong here?

image

byee4 commented 1 year ago

Hi, This might have to do with the untagged version of clipper pointing to a Python2 version. Could you try pulling a later version, which is updated to Python3? eg.

docker://brianyee/clipper:6594e71

cparsania commented 1 year ago

Thanks. It seems working now.

Cheers.

image

s-weissbach commented 1 year ago

I initially thought I cannot use the docker, because I need a newer reference genome (mm39). However, this is not needed during installation and can be added later.

I briefly describe what I did in case someone needs something similar: I did start the container and copied the prepared genome that i created with https://github.com/kopardev/clipperhelper Then copy the gff file to /opt/conda/envs/clipper3/lib/python3.7/site-packages/clipper-2.1.2-py3.7-linux-x86_64.egg/clipper/data and the other two files to /opt/conda/envs/clipper3/lib/python3.7/site-packages/clipper-2.1.2-py3.7-linux-x86_64.egg/clipper/data/regions and you can run the docker file with custom genome.