Error during DangerTrack run

[sean-la]

I've installed DangerTrack on my machine and I'm testing the software. When I run the command sh prepare.sh, I get the following error:

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==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /goldenPath/hg19/encodeDCC/wgEncodeMapability ... done.
==> SIZE wgEncodeDacMapabilityConsensusExcludable.bed.gz ... 4731
==> PASV ... done.    ==> RETR wgEncodeDacMapabilityConsensusExcludable.bed.gz ... done.
Length: 4731 (4.6K) (unauthoritative)

100%[=====================================================================>] 4,731       --.-K/s   in 0.002s  

2017-05-03 11:51:46 (2.29 MB/s) - `wgEncodeDacMapabilityConsensusExcludable.bed.gz' saved [4731]

Error: Unable to open file sv.giab.bed. Exiting.
Error: Unable to open file sv.1kg.bed. Exiting.
prepare.sh: line 98: bigWigAverageOverBed: command not found
prepare.sh: line 99: bigWigAverageOverBed: command not found
cat: wgEncodeCrgMapabilityAlign50mer.5000.txt: No such file or directory
cat: wgEncodeCrgMapabilityAlign100mer.5000.txt: No such file or directory

Thanks in advance!

[igordot]

The BED files should be ungzipped first (they were gzipped for GitHub).

You can download the bigWigAverageOverBed binary (part of UCSC Kent utilities) from http://hgdownload.soe.ucsc.edu/admin/exe/ . There are different builds for different systems, so it's not trivial to just download that automatically.

[sean-la]

That worked, thanks!