FORUMAlign.seqs on Mothur
Genevieve asked 1 year 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 1 year ago

you’re using mothur on galaxy correct?

1 Answers
jrosner Staff answered 1 year 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 1 year 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 1 year 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 1 year 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 1 year ago

OK thank