How to download and set up a Tuberculosis H37rv whole genome in SNPEff software?

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:

snpeff

• 2,194 views • link

updated 9.5 years ago by GenoMax

• written 9.5 years ago by human_genomeXXX •

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.

• 0 views • link

written 9.5 years ago by GenoMax

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