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bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
http://kaiju.binf.ku.dk
GNU General Public License v3.0
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Segmentation fault (core dumped) #277

Open DoreenAA2023 opened 6 months ago

DoreenAA2023 commented 6 months ago

I downloaded refseq database and run kaiju for taxonomic assignment of sample DRR496098 downloaded from SRA, in the kaiju/bin directory using the command below; ./kaiju -t ../../kaiju_db/nodes.dmp -f ../../kaiju_db/kaiju_db_refseq.fmi -i ../../MSB7103_Assignment/raw_data/DRR496098_1.fastq -j ../../MSB7103_Assignment/raw_data/DRR496098_2.fastq -o kaiju_output.txt

I keep getting the error below; Segmentation fault (core dumped)

I made all files in the kaiju/bin readable and executable I have adequate space available, over 500GB

pmenzel commented 6 months ago

How much RAM do you have available? See the README for an estimate of required RAM for each reference database.

DoreenAA2023 commented 6 months ago

My computer has 16 GB of RAM available, I chose refseq database that requires 87 (112) GB RAM.

Aligon1 commented 6 hours ago

I am having this same issue with refseq, how were you able to get it working?