SVachra (Structural Variation Assesment of CHRomosomal Aberrations) is an SV caller for Nextera mate pair sequencing consisting of both inward and outward facing read types. SVachra is a play on the word “chakra” describing the ability to call genomic SV by simultaneously evaluating inward and outward facing read pairs.
Hello I am really keen to try this but not having any joy
Christoss-MacBook-Pro:ruby-2.3.6 christos$ ruby /Volumes/SD/SVachra/SVachra_v1.0.rb /Volumes/Toshiba4Tb/WGSdata/38:14MPS/mayo_MPS/MB/hg38/38_14MB.trimmed.RG.hg38.samblasterdupsemoved.sort.bam
SVachra_v1.0.rb -f reads.bam
optional arguments: -b screen out .bed file (optional)
-c minimun number of non-overlapping read pairs to call breakpoint (DEFAULT=2)
-m minimum mapping quaility threshold (DEFAULT=0)
-n SV annoation name - appended with incrementing integer (DEFAULT=SV)
-u Consider Unique mapping tag (XT:A:U) reads only (optional)
-s SV cluster quality control filter based on proximity overlaps (optional)
help --help [-h]
STARTING: read in ... accumulating insert sizes
/Volumes/SD/SVachra/SVachra_v1.0.rb:1079:in `': Permission denied - /usr/local/Cellar/samtools/ (Errno::EACCES) from /Volumes/SD/SVachra/SVachra_v1.0.rb:1079:in'
I have tried the following
-different Samtools versions 1.3-1.6 ( i changed the path accordingly)
-different Ruby versions the 2.0 that comes wit the Mac, 2.4 via brea, and now 2.3 via ruby-install
I should add that I can't install getoptlong, is this the problem, or permissions do you think>
Christoss-MacBook-Pro:ruby-2.3.6 christos$ gem install getoptlong
ERROR: Could not find a valid gem 'getoptlong' (>= 0) in any repository
Perhaps I should try to use Ruby 1.9.3, would this help? But will I able to find getoptlong?
Hello I am really keen to try this but not having any joy
Christoss-MacBook-Pro:ruby-2.3.6 christos$ ruby /Volumes/SD/SVachra/SVachra_v1.0.rb /Volumes/Toshiba4Tb/WGSdata/38:14MPS/mayo_MPS/MB/hg38/38_14MB.trimmed.RG.hg38.samblasterdupsemoved.sort.bam SVachra_v1.0.rb -f reads.bam optional arguments: -b screen out .bed file (optional) -c minimun number of non-overlapping read pairs to call breakpoint (DEFAULT=2) -m minimum mapping quaility threshold (DEFAULT=0) -n SV annoation name - appended with incrementing integer (DEFAULT=SV) -u Consider Unique mapping tag (XT:A:U) reads only (optional) -s SV cluster quality control filter based on proximity overlaps (optional) help --help [-h] STARTING: read in ... accumulating insert sizes /Volumes/SD/SVachra/SVachra_v1.0.rb:1079:in'
`': Permission denied - /usr/local/Cellar/samtools/ (Errno::EACCES) from /Volumes/SD/SVachra/SVachra_v1.0.rb:1079:inI have tried the following -different Samtools versions 1.3-1.6 ( i changed the path accordingly) -different Ruby versions the 2.0 that comes wit the Mac, 2.4 via brea, and now 2.3 via ruby-install
I should add that I can't install getoptlong, is this the problem, or permissions do you think> Christoss-MacBook-Pro:ruby-2.3.6 christos$ gem install getoptlong ERROR: Could not find a valid gem 'getoptlong' (>= 0) in any repository
Perhaps I should try to use Ruby 1.9.3, would this help? But will I able to find getoptlong?
thanks i n advance if you get the chance to help!
christos