ERROR: failed to generate info file using twoBitInfo

[GoogleCodeExporter]

1) What operating system are you using?
linux
R302
2) What error message was displayed?
ERROR: failed to generate info file using twoBitInfo
3) What was the exact command you used that resulted in the error?
library(zinba)
generateAlignability(
  mapdir = "/michorlab/lliu/Weaver/zinba_utils/", #mappability directory from unpacked mappability files
  outdir = "/michorlab/lliu/Weaver/zinba_output/", #directory for processed files, used later in analysis
  athresh = 1, #number of hits per read allowed during mapping process
  extension = 200, #average fragment library length
  twoBitFile = "/michorlab/lliu/Weaver/zinba_utils/hg19.2bit" #path to downloaded genome build file in .2bit format
)
4) Please copy and paste any additional screen output that resulted from
running the command
Processing chrYb.out .......
    chrY .......

Processing chrYb.out .......
    chrY .......
WARNING: ignoring environment value of R_HOME

ERROR: failed to generate info file using twoBitInfo, twoBit file is: 
/michorlab/lliu/Weaver/zinba_utils/hg19.2bit

Original issue reported on code.google.com by lliu.h...@gmail.com on 6 Dec 2014 at 12:44

[GoogleCodeExporter]

I am wondering whether you had run out of disk space during this process, as a 
large temporary file is often created.  Would this be possible to check?

In the meantime, could you paste the output of the following:  

ls -l /michorlab/lliu/Weaver/zinba_output/
ls -l /michorlab/lliu/Weaver/zinba_utils/
Keep in mind that the  "outdir" folder in this case only should contain the 
files that are generated by generateAlignability, and that mapdir folder should 
simply be the uncompressed contents of the downloaded mappability file 

Original comment by homer...@gmail.com on 26 Jan 2015 at 4:09

[GoogleCodeExporter]

Original comment by homer...@gmail.com on 26 Jan 2015 at 4:48

• Changed state: Accepted