building windows was unsuccssful

GoogleCodeExporter commented 8 years ago

Hi
I am trying to run the version 2.02.03 of zinba and I get the following error

The reason I am trying the new version of zinba is because I have noticed that 
certain chromosomes have no peaks when I used version 2.01, have you come 
across this problem before?

1) What operating system are you using?
  "Linux"          "2.6.32-431.20.3.el6.x86_64" 

2) What error message was displayed?
Processing chrM
    Initializing to length 16571
    Mapping reads to chromosome......
    Getting alignability info from:
        alignallchr/chrM.wig
Unable to open alignability file alignallchr/chrM.wig
Error in buildwindowdata(seq = seq, align = align, input = input, twoBit = 
twoBit,  : 
  ERROR: building windows was unsuccssful
Calls: zinba -> run.zinba -> buildwindowdata -> .C
Execution halted

3) What was the exact command you used that resulted in the error?
library(zinba)
zinba(
  align='alignallchr/',
  numProc=8,
  seq='LIB2804_noM.bed',
  basecountfile='LIB2804_noM.basecount',
  filetype="bed",
  outfile="LIB2804zinba",
  twoBit="/tgac/workarea/users/higginsj/Southgate_CCC_V_16/zinba_map/hg19.2bit",
  extension=120,
  printFullOut=1,
  refinepeaks=1,
  broad=F,
  input="none"
)

4) Please copy and paste any additional screen output that resulted from
running the command

attached

Original issue reported on code.google.com by jhiggin...@gmail.com on 24 Jul 2014 at 8:36

Attachments:

outzim04

GoogleCodeExporter commented 8 years ago

I assume "_noM" means you have eliminated all reads that map to mtDNA.  If you 
also deleted chrM.wig from the alignallchr/ directory, this error makes perfect 
sense.  The reason ZINBA might be trying to find chrM in the alignability 
directory is because its name (and sequence) exists in the 2bit file.  If you 
want a genome that excludes chrM, simply build a FASTA file from the nuclear 
chromosomes in hg19, then use the faToTwoBit program to create a 
mitochondria-free reference genome.  You may have to recompile the alignability 
files with the new genome.

Cheers!

Original comment by pikalax...@gmail.com on 13 Aug 2014 at 10:03

GoogleCodeExporter commented 8 years ago

I have the same issue but for chromosome Y. Since we used female mice only it 
could be possible that only reads for non-Y chromosomes are mapped.

Is there an option that zinba automatically ignores chromosomes that have 0 
reads mapped to it, if not it would be very obnoxious to find out beforehand 
what is mapped and then use a different 2bit file for every omitted chromosome.

Thanks for your help.

PS: Using version 2.03.1

Original comment by lichtenb...@msseeker.org on 3 Apr 2015 at 2:27

sivarajankumar / zinba

building windows was unsuccssful #66