kraken

kraken copied to clipboard

Xargs: cat: terminated by signal 13 with kraken2-build --build.

4

Hello, I am using kraken2 version 2.1.2 and I am trying to build the nt database with the following command: `kraken2-build --build --db /scratch/chauk/kraken2/kraken_nt/nt --threads 48` It fails at step...

kdbchau

Hi. I am having a problem trying to run kmerfinder with the following code: kmerfinder.py -i 899808-assembly-metaSPAdes.fa -db kmerfinder_db/ -tax kmerfinder_db/viral/viral.tax -o test/ but in the terminal it shows me:...

marco315176

Issue with PLASMID download?

2

HI there, while tying to compile the standard database or a custom database with plasmid I receive the error: `gzip: plasmid.1.1.genomic.fna.gz: invalid compressed data--format violated` Should this be downloading from...

axemango

Hi, i am using kraken from a supercomputer using linux. When i try to download de database i get this error kraken2-build --standard --db kraken Downloading nucleotide gb accession to...

jsalas0798

When I was trying to execute the custom build for taxonomy download using below command. I was encountered with below error. Downloading nucleotide gb accession to taxon map...rsync: failed to...

tala-kiyani

when I build the database, I got the following errors: --2023-02-24 09:17:27-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_est.accession2taxid.gz => ‘nucl_est.accession2taxid.gz’ Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 165.112.9.230, 130.14.250.10, 2607:f220:41f:250::229, ... Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.230|:21... connected. Logging in as...

chaoyanggu

kraken-build

18

kraken-build --download-taxonomy --db HumanVirusBacteria bash: /bin/kraken-build: Permission denied and on perl kraken-build --download-taxonomy --db HumanVirusBacteria Can't exec "download_taxonomy.sh": Permission denied at kraken-build line 253

khuch123

problems with building kraken and kraken2 databases

1

Hi, I'm trying to download and build both databases, wanted to use only kraken2 but could do it so tried kraken and got the same error, bellow: can anyone help?...

itiago

building custom database fail at step 5

5

Hi, I have already successfully build custom databases but for some reason, I got an error at step 5 with the following command : kraken-build --threads 40 --build --db ~/kraken_customdb...

dpchris

Dear Karken support team, Why classified reads are contaminated reads? Is it due to the Kraken2 database a database made up of all possible contaminated bacteria? I used the Kraken2...

B-1991-ing