Error generating alignability data

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1) What operating system are you using?

Redhat(TM) / Scientific Linux 5.5 with
Alces HPC Software Stack and R version 2.13.0 

2) What error message was displayed?

ERROR: failed to generate info file using twoBitInfo, twoBit file is: 
../hg18_2bit/hg18.2bit

---------------- ALIGN ADJUST EXITING WITH ERRORS ----------------

3) What was the exact command you used that resulted in the error?

generateAlignability(
mapdir= "../zinba_map_hg18/map36/",      #mappability directory from unpacked 
mappability files
outdir= "SRR088641_zinba/",      #directory for processed files, used later in 
analysis
athresh= 4,     #number of hits per read allowed during mapping process
extension= 200,   #average fragment library length
twoBitFile="../hg18_2bit/hg18.2bit"  #path to downloaded genome build file in 
.2bit format
)

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

> generateAlignability(
+ mapdir= "../zinba_map_hg18/map36/",      #mappability directory from unpacked 
mappability files
+ outdir= "SRR088641_zinba/",      #directory for processed files, used later 
in analysis
+ athresh= 4,     #number of hits per read allowed during mapping process
+ extension= 200,   #average fragment library length
+ twoBitFile="../hg18_2bit/hg18.2bit"  #path to downloaded genome build file in 
.2bit format
+ )

Processing chr10b.out .......
        chr10 .......

Processing chr11b.out .......
        chr11 .......

Processing chr12b.out .......
        chr12 .......

Processing chr13b.out .......
        chr13 .......

Processing chr14b.out .......
        chr14 .......

Processing chr15b.out .......
        chr15 .......

Processing chr16b.out .......
        chr16 .......

Processing chr17b.out .......
        chr17 .......

Processing chr18b.out .......
        chr18 .......

Processing chr19b.out .......
        chr19 .......

Processing chr1b.out .......
        chr1 .......

Processing chr20b.out .......
        chr20 .......

Processing chr21b.out .......
        chr21 .......

Processing chr22b.out .......
        chr22 .......

Processing chr2b.out .......
        chr2 .......

Processing chr3b.out .......
        chr3 .......

Processing chr4b.out .......
        chr4 .......

Processing chr5b.out .......
        chr5 .......

Processing chr6b.out .......
        chr6 .......

Processing chr7b.out .......
        chr7 .......

Processing chr8b.out .......
        chr8 .......

Processing chr9b.out .......
        chr9 .......

Processing chrMb.out .......
        chrM .......

Processing chrXb.out .......
        chrX .......

Processing chrYb.out .......
        chrY .......

Processing chrYb.out .......
        chrY .......

ERROR: failed to generate info file using twoBitInfo, twoBit file is: 
../hg18_2bit/hg18.2bit

---------------- ALIGN ADJUST EXITING WITH ERRORS ----------------

Original issue reported on code.google.com by d.spr...@ed.ac.uk on 3 Oct 2011 at 2:39

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I have also tested the example given in the tutorial and get the same error.  
It would therefore appear to be some problem with the 2bit file or some problem 
using this on my system?

Thanks

Duncan

Original comment by d.spr...@ed.ac.uk on 3 Oct 2011 at 7:50

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Please install this beta version of ZINBA and see if it solves the problem. I 
am in the process of making updates to the current software, and will have this 
release out soon. 

Original comment by homer...@gmail.com on 4 Oct 2011 at 12:00

Attachments:

• zinba_2.01.1.tar.gz

[GoogleCodeExporter]

Original comment by homer...@gmail.com on 7 Oct 2011 at 3:43

• Changed state: Done

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Hi, I tried out the update and it worked. Thanks

Original comment by d.spr...@ed.ac.uk on 10 Oct 2011 at 6:53