conterminator

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Hello team, Would you happen to have a list of identifiers for the predicted contaminations in UniProt? Thanks a lot in advance for your help!! Florian

fmaumusINRA

conterminator frozen at stage rescorediagonal

8

hi, i am trying to test conterminator on a very simple file to start, but it freezes at rescorediagonal stage. When i use example files dna.fas and dna.mapping, everything is...

tougai

Dear @martin-steinegger I am trying to run Conterminator, but I keep getting an error saying "crosstaxonfilterorf step died". I have made my own mapping file, and I also have a...

keishaboateng97

Dear @martin-steinegger , I really like the approach taken in `conterminator` and would like to apply it in my dataset, which is the output of `diamond deepclust`. However, I am...

LotharukpongJS

I donwload nt from ftp.ncbi.nlm.nih.gov:/blast/db/FASTA/nt.gz. Then, make db using: > makeblastdb -in ./nt -dbtype nucl -out ./nt_blast_db Then, run > "$blastdbcmd" -db "$db" -entry all -outfmt "%a %T" > "$taxidmapping"...

maruiqi0710

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...

stas-malavin

Hi, I am trying to clean several de novo assemblies of insects from common contamination sources: human, bacteria and the database UniVec. For this, I concatenated all the fasta in...

HeloiseMuller

Error occurred when building mmseq on Mac

1

Hi, I am trying to install conterminator on Mac by compiling directly from the source code, but errors reported when I tried to build mmseq with using command "make -j...

ywe-1

how to reports contamination with the target sequence is longer than 20kb

1

What can I do if I want to identify a contaminated sequence with a target sequence greater than 20kb? Setting parameters of `./conterminator` or modifying source code when compile it?

lindechun

GTDB

1

Hi, I would love to clean human contaminated sequences from the GTDB bacteria and archaea (r95) and NCBI viruses and fungi, as classifications are being badly affected in some samples...

andrewjmc