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  1. UGENE
  2. UGENE-4880

"ChIP-seq analysis" workflow generates many warnings in the log

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.20
    • Component/s: None
    • Labels:
    • Story Points:
      8
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-02/12/2015
    • Affect Type:
      Userdefined

      Description

      Scenario to reproduce:

      1. Open "ChIP-seq analysis with Cistrome tools" workflow sample.
      2. Run the sample with the next parameters:
        Analysis type: only treatment tags;
        MACS input: "_common_data/NIAID_pipelines/Chip-seq/input_data/chr4.bed".
        Other parameters should be default.
        Current state: log contains many warnings like

        [ERROR][19:00] BED parsing error: incorrect strand value '0' at line 1039!

      Next should be done:

      • Warnings should be shown on the workflow dashboard.
      • It looks like the file that is read with warnings is produced by some tool. Find the reason of warnings and fix it. I suppose that the tool generates a correct file, but UGENE can't read it.
      • Conservation plot doesn't produce a result:

        [ERROR][19:08] conservation plot: Error: unexpected symbol in "plot(x,y0,type="l",col=rainbow(1)[1],main=Average Phastcons"
        [DETAILS][19:08] Tool conservation_plot finished successfully
        [ERROR][19:08] Conservation Plot error: Can not find a required output file /var/folders/c1/vql5jmsj3rd03xlwyd_gzxzw0000gn/T/ugene_tmp/p82504/ConservationPlot_tmp/1445605217_0/tmp.bmp.

      • Conduct GO produces a very suspicious result: the result file contains only several links. The file is attached to the issue.

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              Assignee:
              atiunov Aleksey Tiunov
              Reporter:
              atiunov Aleksey Tiunov
              Assigned Tester:
              Kirill Rasputin
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: