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

Extractframes died (segmentation fault) #21

Open
stas-malavin opened this issue Mar 23, 2023 · 0 comments
Open

Extractframes died (segmentation fault) #21

stas-malavin opened this issue Mar 23, 2023 · 0 comments

Comments

@stas-malavin
Copy link

Hi, I'm trying to reproduce your contamination detection in Trichonephila clavipes spider genome (MWRG01, assembly GCA_002102615.1_NepCla1.0).
I use the following command:

~/Downloads/conterminator/build/bin/conterminator dna GCA_002102615.1_NepCla1.0_genomic.fna MWRG01 spider_result tmp --ncbi-tax-dump ../Aquifers/DB-LINKS/taxonomy

I always get segfault at the extractframes stage, although at a slightly different time, judging by the amount of World Size: 64 dbSize: 0 strings in the log (compare log.txt and log1.txt attached).
I use a self-compiled version (e5d7579, downloaded from github today) and the last NCBI's taxdump. Id mapping file attached.
github-issue.tar.gz

$ cat /etc/*release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.2 LTS"
<...>

Thanks

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

1 participant