Question: QIIME 1.9, make_phylogeny.py: Tree tips not preserved from fasta input
0
gravatar for trichter
7 months ago by
trichter0
trichter0 wrote:

Dear community, i am trying to build a tree with my representative OTU sequences for use with UniFrac.

align_seqs.py -i otus_min3.fa -m muscle -o muscle

The first word of each fasta header in the input file starts with "OTU" and is preserved in the alignment.

head muscle/otus_min3_aligned.fasta

">OTU82968084443698 GTGTCAGCAGCCGCGGTAATACGA----AGGATCCA-

This is used for

make_phylogeny.py -i otus_min3_aligned.fasta -t muscle -o tree

delivering a .tre file, which i want to use with

beta_diversity.py -i ../OTU_TABLE_min3.biom -o beta -m weighted_unifrac -t OTU.tre

The biom file contains the same read names as the alignment input ("OTUnnnnnnnn"). I am now getting this error:

ValueError: No valid samples/environments found. Check whether tree tips match otus/taxa present in samples/environments

Indeed, i found that the tree tips have been renamed as "seqnnnnn".

head OTU.tre

(('seq_2856':0.633333,('seq_2936':0.446667,'seq_5108':0.446667):0.186667):0.62124,((('seq_13435':0.953333,.....

However, the make_phylogeny.py documentation says: "The tips of the tree are the first word from the input sequences from the fasta file, e.g.: ‘>101 PC.481_71 RC:1..220’ is represented in the tree as ‘101’."

This wasnt the case here. Where did i mess up?

ADD COMMENTlink modified 7 months ago • written 7 months ago by trichter0
0
gravatar for trichter
7 months ago by
trichter0
trichter0 wrote:

To give another hint, the default treeing algorithm (-t fasttree) does provide the correct tree tips, while options "mafft" and "muscle" do not.

ADD COMMENTlink written 7 months ago by trichter0
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