# Augur Refine Error **URL:** \ **Category:** Help and Getting Started\ **Created:** [August 9, 2021, 7:35pm UTC](https://nextstrain.discourse.group/t/augur-refine-error/651 "2021-08-09T19:35:02Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![gvestal](https://avatars.discourse-cdn.com/v4/letter/g/e68b1a/32.png) [@gvestal](https://nextstrain.discourse.group/u/gvestal)\ **Post date:** [August 9, 2021, 7:35pm UTC](https://nextstrain.discourse.group/t/augur-refine-error/651/1 "2021-08-09T19:35:02Z")
Running a build with about ~2600 samples. I’ve run into the same error even after downloading the most recent ncov repository from Github. I’ve tried to trouble shoot this, but I’m at a stopping point. I tried do a --latency-wait 1000 and no change. I made a build with ~ 4K samples just before this so I’m not sure what/where to correct. Any feedback would be appreciated. MissingOutputException in line 689 of /nextstrain/build/workflow/snakemake\_rules/main\_workflow.smk: Missing files after 300 seconds: results/TGH/tree.nwk results/TGH/branch\_lengths.json This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Shutting down, this might take some time. ---
**Author:** ![james](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/james/32/11_2.png) [@james](https://nextstrain.discourse.group/u/james)\ **Post date:** [August 10, 2021, 2:38am UTC](https://nextstrain.discourse.group/t/augur-refine-error/651/2 "2021-08-10T02:38:30Z")
Hmm, could you check the output from `logs/refine_TGH.txt` to see if there’s any error printed from the “refine” step? ---
**Author:** ![gvestal](https://avatars.discourse-cdn.com/v4/letter/g/e68b1a/32.png) [@gvestal](https://nextstrain.discourse.group/u/gvestal)\ **Post date:** [August 10, 2021, 3:18am UTC](https://nextstrain.discourse.group/t/augur-refine-error/651/3 "2021-08-10T03:18:58Z")
No error or message of any kind in the logs/refine\_TGH.txt file ---
**Author:** ![gvestal](https://avatars.discourse-cdn.com/v4/letter/g/e68b1a/32.png) [@gvestal](https://nextstrain.discourse.group/u/gvestal)\ **Post date:** [August 10, 2021, 8:22pm UTC](https://nextstrain.discourse.group/t/augur-refine-error/651/4 "2021-08-10T20:22:36Z")
I think the original error was a resource usage error. I changed my Docker usage to --cores 4 and 4GB memory. It pass through, but now there is an error in augur --ancestral. 0.00 -TreeAnc: set-up 8.22 -SequenceData: loaded alignment. 8.23 -SeqData: making compressed alignment… 13.94 -SequenceData: constructed compressed alignment… 13.98 —**WARNING: Number of tips in tree differs from number of sequences in alignment!** 14.03 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0575/2021 14.07 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0298/2021 14.12 \*\*\*WARNING: TreeAnc: 2 nodes don’t have a matching sequence in the alignment. POSSIBLE ERROR. 15.14 -TreeAnc.infer\_ancestral\_sequences with method: probabilistic, joint 15.14 --TreeAnc.\_ml\_anc\_joint: type of reconstruction: Joint 0.00 -TreeAnc: set-up 2.73 -SequenceData: loaded alignment. 2.73 -SeqData: making compressed alignment… 4.76 -SequenceData: constructed compressed alignment… 4.79 —**WARNING: Number of tips in tree differs from number of sequences in alignment!** 4.84 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0804/2021 4.87 \*\*\*WARNING: TreeAnc: 1 nodes don’t have a matching sequence in the alignment. POSSIBLE ERROR. 5.35 -TreeAnc.infer\_ancestral\_sequences with method: probabilistic, joint 5.35 --TreeAnc.\_ml\_anc\_joint: type of reconstruction: Joint 0.00 -TreeAnc: set-up 1.89 -SequenceData: loaded alignment. 1.89 -SeqData: making compressed alignment… 3.12 -SequenceData: constructed compressed alignment… 3.14 —**WARNING: Number of tips in tree differs from number of sequences in alignment!** 3.17 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0792/2021 3.25 \*\*\*WARNING: TreeAnc: 1 nodes don’t have a matching sequence in the alignment. POSSIBLE ERROR. 3.54 -TreeAnc.infer\_ancestral\_sequences with method: probabilistic, joint 3.54 --TreeAnc.\_ml\_anc\_joint: type of reconstruction: Joint 0.00 -TreeAnc: set-up 1.29 -SequenceData: loaded alignment. 1.30 -SeqData: making compressed alignment… 1.61 -SequenceData: constructed compressed alignment… 1.64 —**WARNING: Number of tips in tree differs from number of sequences in alignment!** 1.66 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-BPHL-4996/2021 1.69 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-BPHL-0832/2021 1.71 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/CA-LACPHL-AF00877/2021 1.74 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-BPHL-5006/2021 1.76 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0579/2021 1.79 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0580/2021 1.81 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0689/2021 1.84 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/TN-CDC-4157920-001/2021 1.86 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0756/2021 1.89 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0615/2021 1.91 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0687/2021 1.94 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0762/2021 1.97 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0768/2021 1.99 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/MN-MDH-8330/2021 2.02 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0653/2021 2.04 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0844/2021 2.07 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0784/2021 2.10 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0760/2021 2.13 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0771/2021 2.16 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0818/2021 2.19 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0139/2021 2.23 \*\*\*WARNING: TreeAnc.\_attach\_sequences\_to\_nodes: NO SEQUENCE FOR LEAF: USA/FL-TGH-0531/2021 2.27 \*\*\*WARNING: TreeAnc: 22 nodes don’t have a matching sequence in the alignment. POSSIBLE ERROR. 3.85 -TreeAnc.infer\_ancestral\_sequences with method: probabilistic, joint 3.85 --TreeAnc.\_ml\_anc\_joint: type of reconstruction: Joint 0.00 -TreeAnc: set-up 1.13 -SequenceData: loaded alignment. 1.13 -SeqData: making compressed alignment… 1.29 -SequenceData: constructed compressed alignment… 1.45 -TreeAnc.infer\_ancestral\_sequences with method: probabilistic, joint 1.45 --TreeAnc.\_ml\_anc\_joint: type of reconstruction: Joint 0.00 -TreeAnc: set-up 1.24 -SequenceData: loaded alignment. 1.25 -SeqData: making compressed alignment… 1.58 -SequenceData: constructed compressed alignment… 1.77 -TreeAnc.infer\_ancestral\_sequences with method: probabilistic, joint 1.77 --TreeAnc.\_ml\_anc\_joint: type of reconstruction: Joint [Tue Aug 10 20:11:52 2021] Finished job 17. 19 of 31 steps (61%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message I checked and all of the sequences it mentions were in the original data/sequences.fasta and proper data/metadata.tsv files. If samples are too closely related, would this account for the more intensive CPU usage and errors in tree building?