FORUMAlign.seqs on Mothur
Genevieve asked 3 years 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 3 years ago

you’re using mothur on galaxy correct?

1 Answers
jrosner Staff answered 3 years 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 3 years 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 3 years 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 3 years 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 3 years ago

OK thank