listSRAfile: Error in if (is.na(sra_acc$run[i])) { : argument is of length zero
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Aditya ▴ 120
@aditya-7667
Last seen 6 months ago
Germany

SRAdb::listSRAfile is not working to get SRA file SRX5078836

require(SRAdb)
sqlfile <- getSRAdbFile(destdir = '~/autonomicscache')
sra_con <- dbConnect(SQLite(), sqlfile)
rs <- listSRAfile(c("SRX912152"), sra_con)  # https://www.ncbi.nlm.nih.gov/sra/SRX5078836
                   Error in if is.na(sra_acc$run[i])) { : argument is of length zero

Looks like the database doesn't contain it - any idea why?

sra_acc <- sraConvert("SRX5078836", out_type = c("study", "sample", "experiment", "run"), sra_con = sra_con)
                    [1] experiment study      sample     run       
                        <0 rows> (or 0-length row.names)
SRAdb • 231 views
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