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Kaiju2Table with kbase output

1

Hello. I have been using Kaiju in KBase for my metagenomics data. I was hoping to stitch together all of my output files using Kaiju2table but I'm not sure Kbase...

Jediworm

Building the nr database with low RAM

1

Hi! I would like to use kaiju with the nr database, but I only have access to 12 processor threads and 62 GB of RAM. Is there a way to...

TakacsBertalan

Custom db question

3

Hi, CONTEXT: metagenomic analyses using whole genome seq oxford nanopore data. Samples (15) collected in caves. I want to just focus on plants and bats so I built two different...

valentinavan

kaiju-mkbwt step is always killed

2

output log file: [root@localhost kaiju]# kaiju-mkbwt -n 16 -a ACDEFGHIKLMNPQRSTVWY -o refseq/refseq refseq/kaiju_db_refseq.faa # infilename= refseq/kaiju_db_refseq.faa # outfilename= refseq/refseq # Alphabet= ACDEFGHIKLMNPQRSTVWY # nThreads= 16 # length= 0.000000 # checkpoint=...

DooYal

validity (QC) of prediction files based on a custom reference database

2

Quick question: The resulting prediction file using Kaiju to predict reference genomes of the reads in paired-end FASTQ files includes the taxa IDs from the reference database for some reads...

ramtinz

custom database creation question

1

Hello I want to build my own database (GTDB + own built MAGs). I used prodigal to convert my nucleotide fasta files to protein fasta files. As I see prodigal...

Valentin-Bio-zz

paired end seq are not identical

1

Hi, I am getting error saying that paired end sequences are not identical. Could you give me an idea to overcome this problem?

apoosakkannu

Count dismatch between single kaiju and kaiju-multi

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Hi, Kaiju team. Using a "kaiju-multi" has the same number of lines(reads) in output file as using single "kaiju" ``` wc -l sample.A.kaiju.out > 1635254 wc -l sample.B.kaiju.out > 1949596...

jjuhh

kaiju2table -- Meaning of "cannot be assigned to a (non-viral) X"

9

Problem Description: =============== I'm running the following command:. ```shell kaiju2table -o ./narmena_results.tsv \ -t nodes.dmp \ -n names.dmp \ -r species \ -l superkingdom,phylum,class,order,family,genus,species \ -e *.tsv ``` I'm interested...

LeeBergstrand

kaiju2table and kaiju2krona produce different numbers

2

I have a metagenome from a mixed culture bioreactor enriched in Archaea whose reads I classified using both Kraken2 and Kaiju. I then merged the classifications using the kaiju-mergeOutputs script...

tomberben