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steineggerlab / conterminator

Detection of incorrectly labeled sequences across kingdoms
GNU General Public License v3.0
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Extractframes died (segmentation fault) #21

Open stas-malavin opened 1 year ago

stas-malavin commented 1 year ago

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 (e5d7579c7ab4f8feb78c42ddf00120d235858e7f, 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