Memory cost problem in makedb

Xingyu Luo

New member
I am trying to make database with taxonmap.
Here is my code:
sudo diamond makedb --in /mnt/e/blastdb/nr_database/nr --db nr --taxonmap /mnt/e/diamond/prot.accession2taxid --taxonnames /mnt/e/diamond/taxdmp/names.dmp --threads 4 --taxonnodes /mnt/e/diamond/taxdmp/nodes.dmp

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Is there any way to solve the memory cost problem?
 

Benjamin Buchfink

Administrator
Staff member
The memory use of makedb with taxonomy can be higher than 16 GB unfortunately. It's a known issue and I will try to provide a solution in the future, but it may take some time.
 

Xingyu Luo

New member
I really appreciate the fast reply.
In this case, cause I am going to build a new pc, is it necessary to build the memory with 64GB so that I can makedb with taxonomy, or 32GB is enough.
 

Benjamin Buchfink

Administrator
Staff member
This looks like you are running the native Windows version (diamond.exe). So you should try building the database again using the same call.
 

Xingyu Luo

New member
This looks like you are running the native Windows version (diamond.exe). So you should try building the database again using the same call.
It works! Thanks, really!
So, I don't really know what is going on with the WSL2 and Windows. I asked my friend and he told me it could be the resource distribution of a virtual machine. Also, the install .exe document issue could be caused by the existed Diamond program. I installed it on the WSL2 Linux system, however, the difference between other VM and WSL2 is that WSL2 can "somehow" translate the windows into Linux. That's why I installed Diamond on Linux, but it still can be run with Windows command.
What makes me curious is the Cpu occupation when I run the --makedb commend with -taxonmap. It only takes about 10% at peek. Is there really such a big difference with VM environment?
 
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