Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Segmentation Fault #342

Open
SimonChen1997 opened this issue Apr 24, 2023 · 2 comments
Open

Segmentation Fault #342

SimonChen1997 opened this issue Apr 24, 2023 · 2 comments

Comments

@SimonChen1997
Copy link

SimonChen1997 commented Apr 24, 2023

Hi,

I'm currently doing 6mA methylation detection with megalodon. But there is a issue that I cannot figure out.

The error file for batch running always showed "Segmentation fault".
I also check the log.txt file, which always showed "Could not load guppy server configuration state: 'Configurations'".
The guppy_.log file always ended with "New client connected Client 1 anonymous_client_1 id: 54572796-59e3-4fd4-bc3d-ef59ebc96342 (connection string = 'res_dna_r941_min_modbases-all-context_v001:>timeout_interval=15000>client_name=>barcode_kits=>detect_barcodes=0>move_and_trace_enabled=1>post_out=1')."

I tried to increase the RAM to even 200G, with 28 CPU and 2 GPU. But it didn't work.
Here are my scripts:

megalodon /home/fast5_pass \
--guppy-server-path /home/ont-guppy-gpu-v6.4.2/bin/guppy_basecall_server \
--outputs basecalls mappings mod_mappings mods per_read_mods \
--output-directory /home/mega_out \
--reference /home/GCF_011600945.2_ASM1160094v2_genomic.fna \
--guppy-params "-d /home/rerio/basecall_models/" \
--guppy-config res_dna_r941_min_modbases-all-context_v001.cfg \
--devices "cuda:0,1" \
--processes 1 \
--num-read-enumeration-threads 1 \
--num-extract-signal-processes 1 \
--overwrite

Cheers.

@fsnibs10
Copy link

Hi,

Have you resolved the problem on "segmentation fault" ? I also got the same error information promotting "Segmentation fault (core dumped)". After checking log.txt, the program terminates by promoting "Could not load guppy server configuration state". Are there any other methods to analyze 6mA methylation data? Looking forward to your reply. Thanks.

@SimonChen1997
Copy link
Author

Hi,

Have you resolved the problem on "segmentation fault" ? I also got the same error information promotting "Segmentation fault (core dumped)". After checking log.txt, the program terminates by promoting "Could not load guppy server configuration state". Are there any other methods to analyze 6mA methylation data? Looking forward to your reply. Thanks.

No, I couldn't fix it. I think megalodon has been deprecated by Nanopore, from the previous comment.

#336 (comment)

Cheers

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants