Entering edit mode
7.8 years ago
human_genomeXXX
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10
How to download and set up a Tuberculosis H37rv genome in SNPEff software?
I have tried and it can`t read the reference .gb genome.
How to fix that?
java.lang.RuntimeException: Cannot read file '/home/mat29/Desktop/SRA2SNP_version#5tested_beta_2017_Linuxmint/./data/m_tuberculosis_H37Rv_Broad/genes.gbk'
at ca.mcgill.mcb.pcingola.genBank.FeaturesFile.open(FeaturesFile.java:45)
at ca.mcgill.mcb.pcingola.genBank.FeaturesFile.<init>(FeaturesFile.java:19)
at ca.mcgill.mcb.pcingola.genBank.GenBankFile.<init>(GenBankFile.java:10)
at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGenBank.<init>(SnpEffPredictorFactoryGenBank.java:21)
at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGenBank.<init>(SnpEffPredictorFactoryGenBank.java:16)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:106)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:344)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)
00:00:01 Logging
00:00:02 Checking for updates..
Results with version 4.4:
If you actually have
#
in this path(/home/mat29/Desktop/SRA2SNP_version#5tested_beta_2017_Linuxmint/./data/m_tuberculosis_H37Rv_Broad/genes.gbk)
then you may either want to escape that as/home/mat29/Desktop/SRA2SNP_version\#5tested_beta_2017_Linuxmint/./data/m_tuberculosis_H37Rv_Broad/genes.gbk
or try changing it to some other character and see if that works.Also make sure that the path is valid and the file exists there.