Open mschecht opened 3 days ago
Not a bug from the interface, but there is something wrong with the tree called Rooted final A
. That tree contains less items than what is present in the contigs.db.
# export the bad tree and a good one
$ anvi-export-items-order -p PROFILE.db -o Rooted_final_A.txt --name Rooted_final_A
$ anvi-export-items-order -p PROFILE.db -o IQTree.txt --name IQTree
#count num of item (they all contain 'split')
$ grep -o "split" Rooted_final_A.txt | wc -l
8641
$ grep -o "split" IQTree.txt | wc -l
8682
How is that possible to have a tree with less leafs than items in a profile.db, I have no idea. If you try to re-import the bad tree, anvi'o complains:
$ anvi-import-items-order -p PROFILE.db -i Rooted_final_A.txt --name toto
Target database ..............................: PROFILE.db
Database type ................................: profile
Order file path ..............................: Rooted_final_A.txt
Order data type ..............................: newick
Order name ...................................: toto
Config Error: Ehem. There is something wrong with the incoming items order data here :/
Basically, the names found in your input data do not match to the item names
found in the database. For example, this item
"BATS_SAMN08390924_METAG_Ribosomal_L14_000000000108_split_00001" is in your
database, but not in your input data
Thanks for diving in @FlorianTrigodet! I made a reproducible example with the files attached above. At step 3 is exactly where the number of items in the EVERYTHING bin change from 8,862 → 8,641. It has to do with rotating the tree.
Change items order to IQTree
correct number of leaves
Root here:
correct number of leaves
Rotate here:
Mysteriously 221 leaves disappear :(
Short description of the problem
The number of splits in a bin containing all splits in the interactive interface does not equal the number of items of misc-data.
anvi'o version
System info
macOS Sonoma 14.6.1
Detailed description of the issue
Hi anvi'o community! In my analyses, I use bins to group items that have NA misc-data with their surround splits to pass along information. Unfortunately, I began noticing discrepancies in the number of items of misc-data vs a number of total splits in a collection of all splits i.e when I export a collection containing all splits from a
profile-db
it does not equal the number of items in the misc-data.Here is an example with a bin with everything:
It has 8,641 splits:
You can reproduce the above here:
and load the collection:
IQtree_test_all_bin
(it's a big interface and may take a second to load)However, the number of leaves of the tree and the number of items in the misc-data do not match:
8683 without the headers
Furthermore, the tree in the interface has the same number of leaves at items misc data:
8682 tree tips
I started chatting with @metehaansever about this issue last week but here is the formal documentation of the bug. Thanks in advance for the help and support.
Files / commands to reproduce the issue
https://uchicago.box.com/s/ggg4xso3qxrvdjphsyx006ay1uuzvjcd