Allow for more threads?
punnettsun opened this issue · 9 comments
Hi,
I tried to run the database build, but it seems that my machine is only running MetaCache on a single thread. Is there a way to increase this? I do not see an argument for specifying threads in MetaCache.
Thanks.
I'm sorry, but only the query mode is multi-threaded, the database build is not multi-threaded in version 1.x.x
BTW: This is a limitation that Metacache shares with many other metagenomic classification tools. Kraken2 takes actually even longer for database builds on the same input genome size.
I see. Do you have an estimate for how long it might take to build the complete genomes in RefSeq by any chance?
On our machines it takes a bit more than an hour to build a database containing all complete bacterial, viral and archaea genomes from the latest RefSeq.
Thank you. Can I possibly get your email to email you about the specs I am using to build the database? I have been running on a good machine but the reference sequence processing is still at 0% after 4 hours. I assume this isn't supposed to happen with the machine I am using.
Sure, 4 hours sounds very odd indeed.
I'll have a look at it tomorrow, it's already past 10 pm here :-)
Great thank you!
Did you find any bugs related to this?
I am trying to build a custom database and the build is taking ~50 hours. I am looking for ways to speed this upl
Sorry, but I unfortunately do not have access to the email domain I used at the time to look back at mine and Muellan’s conversation. I believe there was something on my end that was causing the issue with the database build.
I hope you will figure out the issue soon!