Problems with ghost tree import into qiime2

Technical Support
1

Hi All,

I'm trying to use a pre-made ghost tree for an ITS analysis. When I try to import the ghost tree into QIIME2 I'm getting this error:

qiime tools import \

--input-path ghost_tree.nwk
--type Phylogeny[Unrooted]
--output-path ghost-tree-unrooted.qza
There was a problem importing ghost_tree.nwk:

ghost_tree.nwk is not a(n) NewickFormat file

I downloaded the ghost tree using this command (I've included the output as well):

wget ghost-tree-trees/silva-132-foundation/02.02.2019/ghost_tree_80_qiime_ver8_dynamic_02.02.2019/ghost_tree.nwk at master · JTFouquier/ghost-tree-trees · GitHub

--2019-05-21 18:37:45-- ghost-tree-trees/silva-132-foundation/02.02.2019/ghost_tree_80_qiime_ver8_dynamic_02.02.2019/ghost_tree.nwk at master · JTFouquier/ghost-tree-trees · GitHub
Resolving github.com... 192.30.253.113
Connecting to github.com|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: ‘ghost_tree.nwk’

ghost_tree.nwk [ <=> ] 64.92K --.-KB/s in 0.03s

2019-05-21 18:37:45 (2.00 MB/s) - ‘ghost_tree.nwk’ saved [66481]

Does anyone have any suggestions on how to get this working?

1 Like
3

Hello Lauren,

I think i found an important clue!
ghost_tree.nwk [ <=> ] 64.92K --.-KB/s in 0.03s
So the download is 64kb… but the file on github is supposed to be 1.5 MB.

I think the file failed to download!

Try using this link instead (this link should work with wget):

 https://github.com/JTFouquier/ghost-tree-trees/raw/master/silva-132-foundation/02.02.2019/ghost_tree_80_qiime_ver8_dynamic_02.02.2019/ghost_tree.nwk

Colin

2 Likes
5

Sorry you’re having problems importing and sorry for the delay. I’m traveling at the moment but will look into this on Monday. Thank you!

6

Hi Colin,

Good catch! I re-downloaded using wget with the link above and all worked smoothly. Much appreciated!

Lauren

1 Like
7

Great catch Colin, thanks for looking out! When I get a chance to update documentation I will try to clarify the difference between the links.