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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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How to build a custom index (compression)? #232

Open linjiahao962889027 opened 2 years ago

linjiahao962889027 commented 2 years ago

I don't know how to build a custom index. I try to use the following command to build a compression fasta. But it always "Out ofmemory!". centrifuge-compress.pl my.fna taxonomy/ -map seqid2taxid.map -t 32 So how to build a custom index?

sanderdebacker commented 2 years ago

My first thought with the "Out of memory" error, is the lack of RAM on the system running the command. Have you tried again with a smaller "my.fna"?

linjiahao962889027 commented 2 years ago

My first thought with the "Out of memory" error, is the lack of RAM on the system running the command. Have you tried again with a smaller "my.fna"?

Sure, I try many times. Then I split it by taxid and try again, it seems ok. But why the output have only one fasta sequence?