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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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KRAKEN_DB doesnt exist #415

Open rupesh-sinha opened 2 years ago

rupesh-sinha commented 2 years ago

Hi, I am trying to run kraken on my final_assembly_ALL_READS.fasta (command below) but getting an error of KRAKEN_DB doesn't exist. I have run

config-metawrap

and

conda update -y -c ursky metawrap-mg(metawrap-env)

but no luck. I have also run

quast-download-gridss

quast-download-silva

quast-download-busco

out of which busco failed and asked to manually download the files.

The problem is metawrap installation doesn't make any folder called KRAKEN_DB in my home directory.

Any help?

I have copied and pasted the latest kraken command below:

rupesh@elogin04:~/5_Metagenome> metawrap kraken -o KRAKEN2 -t 96 -s 1000000 /home/NCAOR/rupesh/5_Metagenome/assembly/final_assembly_ALL_READS.fasta metawrap kraken -o KRAKEN2 -t 96 -s 1000000 /home/NCAOR/rupesh/5_Metagenome/assembly/final_assembly_ALL_READS.fasta

The folder /home/NCAOR/rupesh/KRAKEN_DB doesnt exist. Please consult the metaWRAP database guite to download and build the KRAKEN database

real 0m0.032s user 0m0.009s sys 0m0.017s

Rooobben commented 2 years ago

Excuse me，did you solve this problem?

I had solved this problem. which config-metawrap opened it with notepad++ and modified it