Open joverlee521 opened 5 months ago
Failure in hmpxv_big build today possibly related to fix_tree.py
, where augur refine
is running into a None
node:
[batch] [2024-03-27T18:00:42+00:00] ERROR: TreeAnc.optimal_branch_length: terminal node alignments required; sequence is missing for leaf: 'None'. Missing terminal sequences can be inferred from sister nodes by rerunning with `reconstruct_tip_states=True` or `--reconstruct-tip-states`
[batch] [2024-03-27T18:00:42+00:00] ERROR from TreeTime: This error is most likely due to a problem with your input data.
[batch] [2024-03-27T18:00:42+00:00] Please check your input data and try again. If you continue to have problems, please open a new issue including
[batch] [2024-03-27T18:00:42+00:00] the original command and the error above: <https://github.com/nextstrain/augur/issues/new/choose>
[batch] [2024-03-27T18:00:42+00:00] augur refine is using TreeTime version 0.11.3
[batch] [2024-03-27T18:00:42+00:00] 367.47 ***WARNING: TreeAnc._check_alignment_tree_gtr_consistency: NO SEQUENCE
[batch] [2024-03-27T18:00:42+00:00] FOR LEAF: 'None'
[batch] [2024-03-27T18:00:42+00:00] 367.50 ***WARNING: TreeAnc: 1 nodes don't have a matching sequence in the
[batch] [2024-03-27T18:00:42+00:00] alignment. POSSIBLE ERROR.
The
hmpxv1_big
build failed yesterday with a validation error fromaugur export v2
I searched for
OP615261
in the results files and see that it only appears once in thetree_raw.nwk
(produced by augur tree) but appears twice in thetree_fixed.nwk
(produced by scripts/fix_tree.py). Somehow scripts/fix_tree.py is duplicating the node.