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  1. UGENE
  2. UGENE-3938

snpEff data path is set incorrecty on Windows

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.16.1
    • Component/s: None
    • Labels:
      None
    • Tests Type:
      GUI automatic
    • Affect Type:
      Userdefined

      Description

      snpEff has the -dataDir parameter that specifies a path for genomes downloaded. It is an internal parameter, in a sense that users do not set it. It is set to .UGENE_downloaded subfolder.

      On Windows this parameter is set in an incorrect way.
      If you run snpEff command like it works on OS X or Linux (C:\Program Files\Java\jre7\bin\java.exe -jar D:\ext_tools_win_64-bit\snpEff-4.0e\snpEff.jar -dataDir C:/Users/WCGW/.UGENE_downloaded\snpeff_data -i vcf -o vcf -upDownS
      treamLen 0 -v testCase D:/UGENE/trunk/test/_common_data/cmdline/external-tool-support/snpeff/annotate_1.vcf) that it causes errors, because the path is concatinated to snpEff executable folder (D:\ext_tools_win_64-bit\snpEff-4.0e\C:\Users\WCGW\.UGENE_downloaded\snpeff_data\testCase\snpEffectPredictor.bin).

      Make sure that on windows the genome data is downloaded to the .UGENE_downloaded subfolder.

      The full log is:
      C:\Users\WCGW>"C:\Program Files\Java\jre7\bin\java.exe" -jar D:\ext_tools_win_64-bit\snpEff-4.0e\snpEff.jar -dataDir C:/Users/WCGW/.UGENE_downloaded\snpeff_data -i vcf -o vcf -upDownStreamLen 0 -v testCase D
      :/UGENE/trunk/test/_common_data/cmdline/external-tool-support/snpeff/annotate_1.vcf
      00:00:00.001 Reading configuration file 'snpEff.config'. Genome: 'testCase'
      00:00:00.527 done
      00:00:00.528 Reading database for genome version 'testCase' from file 'D:\ext_tools_win_64-bit\snpEff-4.0e/C:/Users/WCGW/.UGENE_downloaded\snpeff_data/testCase/snpEffectPredictor.bin' (this might take a w
      hile)
      00:00:00.529 Database not installed
      Attempting to download and install database 'testCase'
      00:00:00.529 Reading configuration file 'snpEff.config'. Genome: 'testCase'
      00:00:00.988 done
      00:00:00.989 Downloading database for 'testCase'
      00:00:00.990 Connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_0/snpEff_v4_0_testCase.zip
      00:00:03.376 Local file name: 'C:\Users\WCGW\AppData\Local\Temp\/snpEff_v4_0_testCase.zip'

      00:00:04.555 Donwload finished. Total 287324 bytes.
      00:00:04.556 Extracting file 'data/testCase/snpEffectPredictor.bin'
      00:00:04.557 Creating local directory: 'D:\ext_tools_win_64-bit\snpEff-4.0e\C:\Users\WCGW\.UGENE_downloaded\snpeff_data\testCase'
      java.lang.RuntimeException: java.io.FileNotFoundException: D:\ext_tools_win_64-bit\snpEff-4.0e\C:\Users\WCGW\.UGENE_downloaded\snpeff_data\testCase\snpEffectPredictor.bin (The filename, directory name, or vo
      lume label syntax is incorrect)
      at ca.mcgill.mcb.pcingola.util.Download.unzip(Download.java:253)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:32)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:85)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:71)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:768)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:299)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:683)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:663)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:734)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:123)
      Caused by: java.io.FileNotFoundException: D:\ext_tools_win_64-bit\snpEff-4.0e\C:\Users\WCGW\.UGENE_downloaded\snpeff_data\testCase\snpEffectPredictor.bin (The filename, directory name, or volume label syntax
      is incorrect)
      at java.io.FileOutputStream.open(Native Method)
      at java.io.FileOutputStream.<init>(Unknown Source)
      at java.io.FileOutputStream.<init>(Unknown Source)
      at ca.mcgill.mcb.pcingola.util.Download.unzip(Download.java:228)
      ... 9 more
      java.lang.RuntimeException: Genome download failed!
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:300)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:683)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:663)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:734)
      at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:123)
      00:00:04.564 Logging
      00:00:05.565 Checking for updates...

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            People

            Assignee:
            kir Kirill Rasputin
            Reporter:
            vaskin Yura Vaskin
            Assigned Tester:
            Ivan Protsyuk
            Watchers:
            3 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: