Conterminator stopped after downloading taxdump.tar.gz

[martin-steinegger]

The command "conterminator dna example/dna.fna example/dna.mapping ${RESULT_PREFIX} tmp" stops while createtaxdb

Download taxdump.tar.gz
tar: Skipping to next header
2020-04-18 14:36:42 URL:https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz [51859296/51859296] -> "-" [7]

gzip: stdin: invalid compressed data--crc error

gzip: stdin: invalid compressed data--length error
tar: Child returned status 1
tar: Error is not recoverable: exiting now
Error: createtaxdb step died

[XiongGZ]

Thank you for this. I think if the taxdump.tar.gz download fail, so createtaxdb step died. Maybe I can download it by myself? But I don't know it should be put in which directory.

[martin-steinegger]

What happens if you download it and unzip on that machine? Does it crash too? Conterminator just uses wget and gunzip.

[XiongGZ]

gunzip? Maybe *.tar.gz file should use tar to unzip? When I use gunzip it just become taxdump.tar ,but I can use command "tar zxvf taxdump.tar.gz" to unzip. I will use the unzip file try again but the unzip files should be saved in which directory?

[XiongGZ]

I see MMseqs2 useage "mmseqs createtaxdb"

Create a seqTaxDB from an existing BLAST database It is easy to create a seqTaxDB from a pre-existing local BLAST databases, if BLAST+ is installed. The following example creates an MMSeqs2 database from NCBI's nt database, but it also works with any of the other BLAST databases including the nr protein database.

First, manually download the NCBI taxonomy database dump:

wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz mkdir taxonomy && tar -xxvf taxdump.tar.gz -C taxonomy

Maybe I should follow these commmands first

[martin-steinegger]

I have added support to provide your own taxdump file. I hope this solves your issue.

mkdir taxonomy/
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
tar xvfz taxdump.tar.gz
cd ..
conterminator dna dna.fas dna.mapping conterm tmp --ncbi-tax-dump taxonomy/

[XiongGZ]

Thanks for your support. I successfully solve the problem.

[chassenr]

Hi @martin-steinegger , I am trying to run conterminator with a local taxdump that I created myself (containing nodes.dmp and names.dmp files). I use the option --ncbi-tax-dump for this. However, conterminator still downloads and uses the taxdump from NCBI (which, of course, does not match with my taxids). Do you have a suggestion how to avoid this behavior?

Thanks!

Cheers, Christiane

[martin-steinegger]

@chassenr what version do you use? This PR should have fixed this issue https://github.com/martin-steinegger/conterminator/pull/7

[chassenr]

@martin-steinegger I used mamba to install conterminator and installed version 1.c74b5. I installed conterminator from source, and now the local taxdump is recognized.

[drelo]

I edited the question since I could resolve this. Sorry I thought I couldn't solve this but I could compile it on my own machine and later on at a cluster.