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asifrim / eXtasy

eXtasy: Variant Prioritization by Genomic Data Fusion
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Run error #4

Open DKPOWA opened 9 years ago

DKPOWA commented 9 years ago

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

' from ./extasy.rb:39:in each' from ./extasy.rb:39:in
'

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

Thanks in advance! Maxi