Genevieve asked 10 months ago
I’m trying align.seqs with the following parameters
-
Input Parameter
Value
Note for rerunfasta – 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 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)
jrosnerHmm… 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
you’re using mothur on galaxy correct?