kaiju

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Error cannot open file

1

I am trying to taxonomically classify my reads using only the viral database. This is the code I used: kaiju -t /home/akhwela/kaijudb/viruses/nodes.dmp -f home/akhwela/kaijudb/viruses/kaiju_db_viruses.fmi \ -i home/akhwela/lustre/Data/noSheepQCRead/*.fastq.gz I keep getting...

akhwela

Is there a way to reduce memory requirement?

4

I would like to thank you so much for this wonderful tool. I really like it so much. However, I would appreciate if there is a way to reduce memory...

aelbehery

Is there any way to convert the kaiju output to the biom format? Short of writing my own code to do it?

najoshi

rec3141

Hi Abigail, For some reason eukdetect gets stuck at the taxonomize stage, i.e., snakemake sleeps and is forever stuck. I thought it was an error with ete3, and even regenerated...

umerijaz

creating custom db causes classification issues

3

So I have created a custom database by taking the refseq proteins and adding proteins from a database called RUG2. When I run classification with the regular refseq database on...

najoshi

unable to custom DB

4

Hello, thank you for creating this amazing tool! I'm trying to custom a uniref90 DB from the uniref90.fsa file. I have made the file has a format like >1_1572043 MEEITQIKKRLSQTVRLEGKEDLLSKKDSITNLKTEEHVSVKKMVISEPKPEKKEDIQLK...

juejun14

Different result from blast hit

4

Dear Developer, Thank you so much for Kaiju. I performed spade assembly (for the virus) and performed kaiju on assembled contigs. For the reference database, I downloaded the viral database...

MonicaSteffi

kaiju-makedb -s nr_euk fails

1

Downloading the nr_euk database using the kaiju-makedb is failing with the following error: Extracting taxdump.tar.gz/... gzip: stdin: invalid compressed data--format violated tar: Unexpected EOF in archive tar: Unexpected EOF in...

ko519

Extracting AA sequences from each sample

4

Hi, I have a question about the Kaiju output. I want to extract the AA sequences derived from fungi from each sample. My goal is to use the sequences as...

andressamv