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  1. UGENE
  2. UGENE-1065

Can't run Bowtie test data on Bowtie in UGENE

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 1.11
    • Fix Version/s: 1.11.2
    • Component/s: None
    • Labels:
      None
    • Tests Type:
      Manual scenario

      Description

      See http://bowtie-bio.sourceforge.net/tutorial.shtml.

      Using the attached test files "e_coli_1000.fa" (reference) and "e_coli_1000.fq" (reads) from the Bowtie package, one can, for example, create an index with the following command:

      bowtie-build e_coli_1000.fa e_coli
      

      and launch Bowtie from the command line as follows:

      bowtie e_coli reads/e_coli_1000.fq
      

      In this case everything works fine and a sam file is created and can be opened in UGENE.

      On the other hand, when Bowtie in launched from the UGENE GUI, a Bowtie error occurs and UGENE informs that Bowtie exited with code "-1073741819" (see screenshots).

      As soon as this issue is fixed, an automated test must be added for this test data!

        Attachments

        1. bowtie_error.png
          bowtie_error.png
          21 kB
        2. bowtie_error_ugene_report.png
          bowtie_error_ugene_report.png
          20 kB
        3. e_coli_1000.fa
          41 kB
        4. e_coli_1000.fq
          78 kB

          Activity

            People

            Assignee:
            kokonech Konstantin Okonechnikov (Inactive)
            Reporter:
            oigl Olga Golosova
            Assigned Tester:
            Aleksey Tiunov [X] (Inactive)
            Watchers:
            1 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: