asifrim / extasy Goto Github PK

Whenever I try to use eXstasy I get this error, probably due to a wrong argument passing to randomForest package:

$ ./extasy.rb -i 148.vcf -g geneprios/res/HP_0008872_fgs.tsv,geneprios/res/HP_0001249_fgs.tsv,geneprios/res/HP_0004322_fgs.tsv,geneprios/res/HP_0001999_fgs.tsv  -c
2014-05-31 15:08:01 +0200: Sorting input VCF...
2014-05-31 15:08:01 +0200: Input VCF sorted...
2014-05-31 15:08:01 +0200: Finding missense mutations...
2014-05-31 15:08:35 +0200: Fetching features for variants...
2014-05-31 15:08:36 +0200: 50 missense variants annotated...
2014-05-31 15:08:36 +0200: Prioritizing against geneprios/res/HP_0008872_fgs.tsv
2014-05-31 15:08:36 +0200: Appending gene prioritization data...
2014-05-31 15:08:37 +0200: Data ready for eXtasy...
2014-05-31 15:08:37 +0200: Running eXtasy...
randomForest 4.6-7
Type rfNews() to see new features/changes/bug fixes.
Error in predict.randomForest(rf, d, type = "prob") : 
  New factor levels not present in the training data
Calls: predict -> predict.randomForest
Execution halted

This is my R configuration

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RobustRankAggreg_1.1 randomForest_4.6-7  

loaded via a namespace (and not attached):
[1] tcltk_3.1.0 tools_3.1.0

Hello, just started with eXtasy, I think I`ve installed everything properly, but when I try to run it:

maxi@InfoMaxi:~/Downloads/Genoma/eXtasy-0.1$ ./extasy.rb -i /home/maxi/Downloads/Genoma/VCF/miller.vcf -g ./geneprios/res/HP_0007477_fgs.tsv
2015-10-27 12:19:34 -0300: Sorting input VCF...
/home/maxi/Downloads/Genoma/eXtasy-0.1/intersectbed.rb:5: warning: Insecure world writable dir /home/maxi/Downloads/Genoma/anntools in PATH, mode 042777
2015-10-27 12:19:34 -0300: Input VCF sorted...
2015-10-27 12:19:34 -0300: Finding missense mutations...
Error: unable to open file or unable to determine types for file /home/maxi/Downloads/Genoma/VCF/miller.vcf.sorted
2015-10-27 12:19:34 -0300: Fetching features for variants...
2015-10-27 12:19:34 -0300: 0 missense variants annotated...
2015-10-27 12:19:34 -0300: Prioritizing against ./geneprios/res/HP_0007477_fgs.tsv
2015-10-27 12:19:34 -0300: Appending gene prioritization data...
2015-10-27 12:19:35 -0300: Data ready for eXtasy...
2015-10-27 12:19:35 -0300: Running eXtasy...
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.
Error in $<-.data.frame(*tmp*, "altbase", value = "T") :
replacement has 1 row, data has 0
Calls: $<- -> $<-.data.frame
Execution halted
2015-10-27 12:20:07 -0300: eXtasy prioritization completed!
./extasy.rb:52:in rename': No such file or directory @ sys_fail2 - (/home/maxi/Downloads/Genoma/VCF/miller.vcf.sorted.matches.annotated.extasy_input.extasy_output, /home/maxi/Downloads/Genoma/VCF/miller_-_HP_0007477_fgs.extasy) (Errno::ENOENT) from ./extasy.rb:52:inblock in

The vcf seems fine, so I dont know what might be causing this.

Thanks in advance!
Maxi

$ ./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 $<-.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:in rename': 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 in

I 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 $<-.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:in rename': 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 in

Would you suggest me some hint to solve this?
I'm using eXtasy in commit

$ git rev-parse HEAD
f977228

$ 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

I just wondering how you deal with swissprot function annotation and whether you have the data in your repo...

Thanks