Hi Ana, The first error message may be the critical one. "weight//NA" is almost certainly not the name of the file you want, and two consecutive slashes in a path is also incorrect. You may not have placed the data files in the correct file structure, often a problem with programs that are written with hard path codings. Without actually trying to download the data and run the script, that is about all the assistance I can provide. If you know someone who has successfully run it, you may be able to get more specific advice.
Jim On Wed, Jul 10, 2019 at 1:32 AM Ana Marija <sokovic.anamar...@gmail.com> wrote: > > Hello, > > I am trying to run this program FUSION.assoc_test.R from : > http://gusevlab.org/projects/fusion/#typical-analysis-and-output > > [t.cri.asokovic@cri16in002 fusion_twas-master]$ Rscript FUSION.assoc_test.R > \ > > --sumstats /gpfs/data/stranger-lab/anamaria/meta_gwas/META_CHR22_1.txt \ > > --weights ./weight/retina.pos \ > > --weights_dir ./weight/ \ > > --ref_ld_chr ./LDREF/1000G.EUR.22 \ > > --chr 22 \ > > --out PGC2.SCZ.22.dat > Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection > Calls: load -> readChar > In addition: Warning message: > In readChar(con, 5L, useBytes = TRUE) : > cannot open compressed file './weight//NA', probable reason 'No such file > or directory' > Execution halted > > I also formatted my retina.pos to be the same as in the given example (the > example does run for me) > > WGT ID CHR P0 P1 > retina/retina.ENSG00000000419.wgt.RDat DPM1 chr20 50934867 > 50958555 > retina/retina.ENSG00000000457.wgt.RDat SCYL3 chr1 169849631 > 169894267 > retina/retina.ENSG00000000460.wgt.RDat C1orf112 chr1 169662007 > 169854080 > retina/retina.ENSG00000000938.wgt.RDat FGR chr1 27612064 > 27635277 > retina/retina.ENSG00000000971.wgt.RDat CFH chr1 196651878 > 196747504 > > > [t.cri.asokovic@cri16in002 weight]$ ls > retina retina.pos > [t.cri.asokovic@cri16in002 weight]$ pwd > /gpfs/data/stranger-lab/anamaria/fusion/fusion_twas-master/weight > > in retina folder I have all .RDat files > > Does anyone know what is the issue here? It is impossible to get an answer > from the developer. > > Thanks > Ana > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
