R session aborted when using assignTaxonomy.

[zo88]

Hi,

My R session keeps crashing when I try to assign taxonomy.

Here is the code I am trying to run: Test_blocking.nochim.tax <- assignTaxonomy(Test_blocking.nochim, "/.../MIDORI_UNIQ_NUC_SP_GB249_CO1_DADA2.fasta", multithread=TRUE)

Here are the versions of dada2 and R I am using.

I don't think it comes from a memory issue because I have 16 Go RAM.

Does anybody know where it could come ?

Thank you for your help

[benjjneb]

It's probably a memory issue, or a databse format issue (as that doesn't look like one of our standard databases), or a combination of the two.

How was that reference file created? How many sequences are in that reference file? Can you post what the first few header lines look like? Has someone else used it successfully on their machine?

[zo88]

That reference file comes from the MIDORI database and it is supposed to me formatted for dada2.

[benjjneb]

Can you post the full ID lines, not just the beginnings?

When you say it "comes from the MIDORI database" -- this is released by the MIDORI database folks? Or, someone created this file themselves out of the MIDORI database? If the former, I'd ask someone there what sort of memory requirements are needed to use it with DADA2.

[zo88]

It was released by the MIDORI team.

[benjjneb]

Format looks OK. Is there a link to this file? So I can try it out on my own machine.

As for the memory issue, I would reach out to the MIDORI team that released it and ask if they have any guidance on the amount of memory needed to use this reference. It is not unlikely that it could require more than 16GB given that this goes all the way down to the species-level, rather than stopping at the genus level, which means there are more unique taxonomies and thus higher memory requirements.