CODEWITHSUNDEEP
r
user3105519
user3105519

Reputation: 309

Tax4Fun...Error in gzfile(file, “wb”): cannot open the connection or compressed file

I am running a microbial predictive functional profiling script and having this strange error. Here is my code: 

file <- "HMP_0.97_table.txt"
QIIMESingleData <- importQIIMEData(file)
folderReferenceData <- "~/SILVA119/"
Tax4FunOutput <- Tax4Fun(QIIMESingleData, folderReferenceData, fctProfiling = TRUE, refProfile = "UProC", shortReadMode = TRUE, normCopyNo = TRUE)

Error in gzfile(file, "rb") : cannot open the connection In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/Users/person/SILVA119/KEGGBacArchTaxInformationMoPPro.RData', probable reason 'No such file or directory'

I check my working directory with getwd and it says 

getwd()
[1] "/Users/person/Downloads/Tax4FunData/SILVA119"

None of the files in the folder are compressed. I also noticed when I try opening the Rdata file R Studio gives me the following error:

load("/Users/person/Downloads/Tax4FunData/SILVA119/PathwayAbundancesKEGGBacArch.RData")

Error: bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘PathwayAbundancesKEGGBacArch.RData’ has magic number 'X' Use of save versions prior to 2 is deprecated

So I'm really unsure of how to proceed here. Here is the session data: 

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] Tax4Fun_0.3.1 biom_0.3.12   qiimer_0.9.2  Matrix_1.2-2 

loaded via a namespace (and not attached):
 [1] colorspace_1.2-6   scales_0.3.0       plyr_1.8.3        
 [4] tools_3.2.2        gtable_0.1.2       RColorBrewer_1.1-2
 [7] Rcpp_0.12.2        RJSONIO_1.3-0      grid_3.2.2        
[10] munsell_0.4.2      lattice_0.20-33    pheatmap_1.0.7    
>

Upvotes: 0

Views: 3671

Answers (1)

hrbrmstr
hrbrmstr

Reputation: 78792

This is a pretty wonky package. The following works perfectly for me, but you really need to look at other SO questions to see what a minimal reproducible example looks like (it's very unlikely that your next SO question will get an answer without you showing some minimal effort):

devtools::install_url("http://tax4fun.gobics.de/Tax4Fun/Tax4Fun_0.3.1.tar.gz")

library(Tax4Fun)

download.file("http://tax4fun.gobics.de/Tax4Fun/ReferenceData/SILVA119.zip", "SILVA119.zip")
unzip("SILVA119.zip")

download.file("http://tax4fun.gobics.de/QIIME/HMP_0.97_table.txt", "HMP_0.97_table.txt")
file <- "HMP_0.97_table.txt"

QIIMESingleData <- importQIIMEData(file)

 # SO is my dir for SO answer work

folderReferenceData <- "~/SO/SILVA119/"
Tax4FunOutput <- Tax4Fun(QIIMESingleData, folderReferenceData, fctProfiling = TRUE, refProfile = "UProC", shortReadMode = TRUE, normCopyNo = TRUE)

Upvotes: 1

Related Questions