Question: align.seq mothur error
gravatar for rizkyana.avissa
9 weeks ago by
rizkyana.avissa0 wrote:

Hi. i am new to galaxy. i'm trying to align my NGS samples based on galaxy 16s Microbial Analysis with Mothur tutorial, my sample use V1-V2 region, so i thought it would be wrong if i use silva.v4.fasta as the reference. i went to silva website, download a reference file and upload it to galaxy, which is SILVA_132_SSURef_Nr99_tax_silva.fasta .

when i try to align my unique.seqs with the reference using align.seq, all parameter default, it comes to an error with message "term environment variable not set". i am trying to check the error details, but i get no other explanation in bug report. it only show this :

Dataset Error
An error occured while running the tool

Tool execution generated the following messages:

Fatal error: Exit code 1 ()
TERM environment variable not set.
TERM environment variable not set

what might i do wrong? should the reference and the sample data be in approximately same length?

error silva alignment mothur • 149 views
ADD COMMENTlink modified 8 weeks ago by Jennifer Hillman Jackson25k • written 9 weeks ago by rizkyana.avissa0

For reference, the tutorial link:

ADD REPLYlink written 8 weeks ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
8 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


The fasta dataset chosen will not work as a reference dataset with Align.seqs. The technical reason for the error is related to that data's content.

Error: Reading in the alignment.reference.dat template sequences... [ERROR]: template is not aligned, aborting.

Appropriate fasta template targets are listed here: >>

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Jennifer Hillman Jackson25k
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