FORUMAlign.seqs on Mothur
Genevieve asked 10 months ago

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

    • Input Parameter
      Note for rerun

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

      Select Reference Template from

      reference – Reference to align with
      101: UNITE.fasta

      Select a search method

      ksize – kmer length between 5 and 12

      align – Select a pairwise alignment method
      needleman (default)

      Alignment scoring values

      flip – Try to align against the reverse complement

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

    jrosner Staff replied 10 months ago

    you’re using mothur on galaxy correct?

    1 Answers
    jrosner Staff answered 10 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 10 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 10 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 10 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 10 months ago

    OK thank