kaiju

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The download of Mar metadata fails at ``` Downloading MarRef metadata from MMP (databasesapi.sfb.uit.no) ``` I think it's a problem with the line ``` MARREF_VERSION=$(curl -Ls -o /dev/null -w %{url_effective}...

pmenzel

Identifying optimized values for `m` and `s`

1

Hi! I'm interested in using kaiju to identify fungi in my metagenomic short reads. However, when I use the default parameters, I get essentially the same profile of fungi across...

ktmbiome

Stuck at the last step of makedb

3

Hi I have a question about the step of Creating the reference database and index Here is my output log file I used 5 cores, RAM of 800G and a...

AlexSongh

Failure to creating the reference database and index of nr_euk

4

Hi I have a problem when downloading the euk_nr database using the slurm scripts I have installed a kaiju conda environment, and run the following codes My HPC settings were...

AlexSongh

Custom DB Issue

3

I want to create a custom database using GTDB (genome taxonomy databse) where the protein sequences are identified by their accession number. I wrote a python script to find the...

shaylashahar

770904 killed ./kaiju -z 64 -t nodes.dmp -f kaiju_db_nr.fmi -i -j -o kaiju_1.out

2

Hello,thank you for this useful tool, I use this command line: ./kaiju -z 64 -t nodes.dmp -f kaiju_db_nr.fmi -i /data1/qinjunjun/zhu_bingduzu/clean_data/1_final_R1.fastq.gz -j /data1/qinjunjun/zhu_bingduzu/clean_data/1_final_R2.fastq.gz -o kaiju_1.out [1] 770904 killed ./kaiju -z 64...

qinjunjun

resume/continue

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Hi! Is it possible in kaiju to continue the classification interrupted? For example, the classification is being recorded and suddenly the electricity is turned off. Naturally, the computer shuts down,...

Mewgia

how to use multiple databases and generate krona.html and bubbles.svg?

1

Hi, I have been using kaiju recently and want to use the virus, plasmids and fungi databases from here: https://kaiju.binf.ku.dk/server I downloaded the databases `.tgz` files and put each `kaiju_db_*.fmi`,...

AravindPattisapu

kaiju-makedb for mar database

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Hi, I've been trying to set up the mar database for a metagenomics project, but I've been running into two odd issues: 1. Sometimes, when installing the database (I've found...

ThijsSt

Taxonomic Annotation from orfs

1

Hi all, Sorry if this question is silly. I have several fasta files from some kegg orthogoly of my interest which I extracted from prodigal and hmmsearch result. For example,...

tpellegrinetti