1) What operating system are you using?
Linux (on Ubuntu virtual machine)
2) What error message was displayed?
Processing chr22
Initializing to length 49691432
Mapping reads to chromosome......
Getting alignability info from:
align_athresh4_extension134/chr22.wig
Unable to open alignability file align_athresh4_extension134/chr22.wig
ERROR: building windows was unsuccssful
--------BUILD WINDOWS COMPLETE-------
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
cannot open file 'data/faire_files/faire.list': No such file or directory
3) What was the exact command you used that resulted in the error?
>
zinba(align='align_athresh4_extension134/',numProc=4,seq='data/faireGM12878rep1c
hr22.taf',basecountfile='data/faireGM12878rep1chr22.basecount',filetype="tagAlig
n",outfile="data/faire",twoBit="hg18.2bit",extension=134,printFullOut=1,refinepe
aks=1,broad=F,input="none")
4) Please copy and paste any additional screen output that resulted from
running the command
When I scrolled through the previous commands, I noticed that the
generateAlignability process hadn't completed (exact command below).
It processed all the chr#b.out files, but only "printed out" and created the
.wig files for chr10-chr19 (output below).
>
generateAlignability(mapdir='map36/',outdir='align_athresh4_extension134/',athre
sh=4,extension=134,twoBitFile='hg18.2bit')
.
.
.
Loading align count data from map36/temp.wig
Processing chr10
Printing output to: align_athresh4_extension134/chr10.wig
Processing chr11
Printing output to: align_athresh4_extension134/chr11.wig
Processing chr12
Printing output to: align_athresh4_extension134/chr12.wig
Processing chr13
Printing output to: align_athresh4_extension134/chr13.wig
Processing chr14
Printing output to: align_athresh4_extension134/chr14.wig
Processing chr15
Printing output to: align_athresh4_extension134/chr15.wig
Processing chr16
Printing output to: align_athresh4_extension134/chr16.wig
Processing chr17
Printing output to: align_athresh4_extension134/chr17.wig
Processing chr18
Printing output to: align_athresh4_extension134/chr18.wig
Processing chr19
Printing output to: align_athresh4_extension134/chr19.wig
---------------- ALIGN ADJUST COMPLETED SUCCESSFULLY ----------------
Original issue reported on code.google.com by liz.goos...@gmail.com on 30 Oct 2013 at 4:35
Original issue reported on code.google.com by
liz.goos...@gmail.com
on 30 Oct 2013 at 4:35