Dear professor,

When trying to use the astalavista (version 3.1) on our linux server, I encounter a problem as follow. It seems that the software got some errors but it finally run and get the result. I want to konw why the ERROR warnings happened, and how to fix them.

Thank you very much!

Yours sincerely,

Yanting Shen

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6 Comments

  1. Micha Sammeth

    Dear Yanting,

    I think the error is related to the issue reported BARNA-288 - Getting issue details... STATUS

    Please see if running the program with a fully qualified path removes the error.

    Best,

    Micha

    1. Yanting Shen

      Dear Micha,
       
      Thanks very much for your quick reply.
       
      I have tried to run the astalavista with a fully qualified path, like this:
      [ytshen@IGDBTIANLAB bin]$ /home/ytshen/tools/astalavista-3.1/bin/astalavista -t asta -i /home/ytshen/analysis_data/cufflinks/2013-4-9/coty_default/final_parameter/transcripts.gtf -o test.asta
      but I got the same errors again.
       
      Please pay attention to that do not like the reporter you quote before, it seems that I can launch the astalavista and get the result finally. It just some error warnings before launch the astalavista.
      Look forward for your help! Thank you very much!
       
      All the best
      Yanting Shen

      1. Thasso Griebel

        Hi,

        turns out it is indeed another problem. We are looking into this right now ( BARNA-304 - Getting issue details... STATUS )

        1. Yanting Shen

          Hi,

          Thank you very much, Maybe you can inform me when the problem resolved. 

  2. Micha Sammeth

    Hi Yanting,

    yes indeed, the phenomenon was actually introduced when integrating the splice site scorer functionality in AStalavista version 3.1. However, in my tests the warning had no influence on the results produced by the program. If you do not use splice site scoring ou may equivalently also use version 3.0 of the program which does not show the warning.

    As ticket BARNA-304 has been resolved, we are to build an update release soon. 

    1. Yanting Shen

      Hi Micha,

      Thank you very much! Looking forword to the updata release.