FORUMAlign.seqs on Mothur
Genevieve asked 6 months ago



  • I’m trying align.seqs with the following parameters 

    • Input Parameter
      Value
      Note for rerun

      fasta – Candiate Sequences
      92: Unique.seqs on data 87: fasta
       

      Select Reference Template from
      history
       

      reference – Reference to align with
      101: UNITE.fasta
       

      Select a search method
      kmer
       

      ksize – kmer length between 5 and 12
      8
       

      align – Select a pairwise alignment method
      needleman (default)
       

      Alignment scoring values
      no
       

      flip – Try to align against the reverse complement
      no

    and i got an error : TERM environment variable not set
    Someone can help me with this ?

    jrosner Staff replied 6 months ago

    you’re using mothur on galaxy correct?

    1 Answers
    jrosner Staff answered 6 months ago



  • Hi Genevieve,
    This error usually comes up in Galaxy when one of the input datasets has no content.  Can you make sure that all inputs have content and that they’re actively loaded into your history?

    Genevieve replied 6 months ago

    Yes all my input file has a content and they are in my history. I have 777,113 sequences in the UNITE fasta file and the other file is my unique.seq fasta file.

    Genevieve replied 6 months ago

    I also tried with the UNITE_public_mothur_full_01.12.2017.fasta as Reference to align with and I got the same error (TERM environment variable not set)

    jrosner Staff replied 6 months ago

    Hmm… I was going to suggest you post your issue to the Galaxy forum on Biostars, but i see you’ve already done this!
    This might be the way to go since they can access your session and debug directly, however if you don’t get a response in the next few days, you could perhaps send me your data and I’ll try to reproduce the error.
    sound good?

    Genevieve replied 6 months ago

    OK thank