asifrim
commented
10 years ago Trying to reproduce running environment, eXtasy has not been tested on Ruby 2.x or in a Mac environment.
Open asifrim opened 10 years ago
asifrim
commented
10 years ago Trying to reproduce running environment, eXtasy has not been tested on Ruby 2.x or in a Mac environment.
$ ./extasy.rb -i myfile.vcf -g ./geneprios/res/HP_0002863_fgs.tsv -k 2013-11-15 14:45:10 +0100: Sorting input VCF... 2013-11-15 14:45:10 +0100: Input VCF sorted... 2013-11-15 14:45:10 +0100: Finding missense mutations... 2013-11-15 14:45:52 +0100: Fetching features for variants... 2013-11-15 14:45:53 +0100: 0 missense variants annotated... 2013-11-15 14:45:53 +0100: Prioritizing against ./geneprios/res/HP_0002863_fgs.tsv 2013-11-15 14:45:53 +0100: Appending gene prioritization data... 2013-11-15 14:45:54 +0100: Data ready for eXtasy... 2013-11-15 14:45:54 +0100: Running eXtasy... randomForest 4.6-7 Type rfNews() to see new features/changes/bug fixes. Error in'
from ./extasy.rb:39:in '
$<-.data.frame(*tmp*, "altbase", value = "T") : replacement has 1 row, data has 0 Calls: $<- -> $<-.data.frame Execution halted 2013-11-15 14:46:01 +0100: eXtasy prioritization completed! ./extasy.rb:52:inrename': No such file or directory - (myfile.vcf.sorted.matches.annotated.extasy_input.extasy_output, myfile_-_HP_0002863_fgs.extasy) (Errno::ENOENT) from ./extasy.rb:52:inblock ineach' from ./extasy.rb:39:inI know variants included in my vcf (which come from an exome sequencing study) contain some missense mutations. I've tried eXtasy with example data and I get the very same error:
$ ./extasy.rb -i example_data/example.vcf -g ./geneprios/res/HP_0002863_fgs.tsv -k 2013-11-15 14:47:56 +0100: Sorting input VCF... 2013-11-15 14:47:56 +0100: Input VCF sorted... 2013-11-15 14:47:56 +0100: Finding missense mutations... 2013-11-15 14:48:16 +0100: Fetching features for variants... 2013-11-15 14:48:17 +0100: 0 missense variants annotated... 2013-11-15 14:48:17 +0100: Prioritizing against ./geneprios/res/HP_0002863_fgs.tsv 2013-11-15 14:48:17 +0100: Appending gene prioritization data... 2013-11-15 14:48:18 +0100: Data ready for eXtasy... 2013-11-15 14:48:18 +0100: Running eXtasy... randomForest 4.6-7 Type rfNews() to see new features/changes/bug fixes. Error in'
from ./extasy.rb:39:in '
$<-.data.frame(*tmp*, "altbase", value = "T") : replacement has 1 row, data has 0 Calls: $<- -> $<-.data.frame Execution halted 2013-11-15 14:48:26 +0100: eXtasy prioritization completed! ./extasy.rb:52:inrename': No such file or directory - (example_data/example.vcf.sorted.matches.annotated.extasy_input.extasy_output, example_data/example_-_HP_0002863_fgs.extasy) (Errno::ENOENT) from ./extasy.rb:52:inblock ineach' from ./extasy.rb:39:inWould you suggest me some hint to solve this? I'm using eXtasy in commit
$ git rev-parse HEAD f97722858ed7924665be05cff514110b94ffeb49
$ git describe --tags 0.1-2-gf977228
$ ruby -v ruby 2.0.0p247 (2013-06-27 revision 41674) [universal.x86_64-darwin13]
$ uname -a Darwin rs800007.station 13.0.0 Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64 x86_64