Comments (2)
@yenagra I wouldn't worry about the harddrive. phylostratr
only uses proteomes and these tend to only require tens of megabytes. So as long as you have a few free GB, you will be fine.
You are far more likely to run into memory problems. I can just barely run Arabidopsis thaliana test case on my desktop, where I have 8 GB of RAM. So currently you may need to run phylostratr
on a server if you are doing a large study.
There is certainly a lot of room for improvement in the phylostratr
implementation. I could replace the in-memory data structures with a SQLite database. That would basically solve the memory problem.
The other performance issue to consider is the time required to BLAST everything. You will likely want to run the BLASTs on a server and phylostratr
currently doesn't automate this. Though handling high-performance computation in R is totally possible.
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That's good, thanks.
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Related Issues (20)
- Issue in compiling phylostratr results HOT 2
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- Error in readLines(con) : HTTP error 400. HOT 14
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- Error in (function (fastafile, blastdb = "blastdb", verbose = FALSE) : Failed to make blast database blastdb/Araport11_genes.201606.pep.fasta In addition: Warning message: In system2("makeblastdb", stderr = TRUE, stdout = TRUE, args = c("-dbtype", : running command '"makeblastdb" -dbtype prot -in Araport11_genes.201606.pep.fasta -out blastdb/Araport11_genes.201606.pep.fasta' had status 1 HOT 10
- Error in if (class(strata) != "Strata") { : the condition has length > 1 HOT 1
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