Open SilSanGon opened 3 months ago
Hi,
Please post the output of running
sessionInfo()
and system2("blastn", "-version")
after all used packages are loaded.
Can you run the example in the man page successfully?
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
package = "rBLAST"))[1]
seq
cl <- predict(bl, seq)
cl[1:5, ]
Regards, Michael
Hi,
Okey, I post the output
Yes, I can run the example in the man page successfully, I post too
I could do it, but it is heavy. How can I send it?
Maybe, I think, is it possible that the 16S_rRNA_DB database is not compatible with the readDNAStringSet() function? I'm testing with this function and not with readRNAStringSet()
Thank you very much! Silvia
OK, let me know.
Hi Michael,
I was looking for a solution and I found that it wouldn't be a problem use 16S_rRNA database with readDNAStringSet() function in this post (https://bioinformatics.stackexchange.com/questions/4015/is-it-ok-to-use-blast-to-query-ncbis-16s-rrna-database-with-16s-dna-sequences) so what do you think it could be the problem?
I have tried to attach the script with a sample and it is impossible because it weighs more than 25Mb. Do you know other way?
Can you put the data and the script on google drive and share it with me? mhahsler@gmail.com
Hello!
I want to analyse my samples against 16S NCBI database, which I downloaded previously, but when I tried the last step, function predict(), its takes 5 days without results. Do you know what is the cause? or if I did something wrong?
I copy my code in:
start blast steps
seq <- readDNAStringSet("All_combined_seqs.fasta")
Make BLAST db and perform BLAST search
makeblastdb(path_to_seqs4_BLAST_db, dbtype = "nucl") dbb <- blast(db=path_to_seqs4_BLAST_db)
tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz") untar(tgz_file, exdir = "16S_rRNA_DB")
Load the downloaded BLAST database.
bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA") bl
change parameters here as required
results = predict(bl, seq, BLAST_args= c("-perc_identity 99")) write.csv(results, "blast_results.csv", row.names = FALSE)
My computer is Ubuntu 22.04.2, AMD Ryzen threadripper 1920x 12-core processor x24, 500GB of memory. Thank you very much in advance!