# Augur Refine fails but does not generate an error log **URL:** \ **Category:** Help and Getting Started\ **Created:** [April 9, 2021, 6:57pm UTC](https://nextstrain.discourse.group/t/augur-refine-fails-but-does-not-generate-an-error-log/479 "2021-04-09T18:57:29Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![MaartenVanDiest](https://avatars.discourse-cdn.com/v4/letter/m/76d3ee/32.png) [@MaartenVanDiest](https://nextstrain.discourse.group/u/MaartenVanDiest)\ **Post date:** [April 9, 2021, 6:57pm UTC](https://nextstrain.discourse.group/t/augur-refine-fails-but-does-not-generate-an-error-log/479/1 "2021-04-09T18:57:29Z")
Hi everyone, I am currently trying to make a Louisiana focused build using data from Gisaid and their North-America focused build as multiple inputs. After some f trial and error with formatting the input data, I got to the tree refinement. When running the command it will run for about an hour and then fails without an error log or error message. The output is shown below ![image](https://canada1.discourse-cdn.com/flex031/uploads/nextstrain/original/1X/c15828c0eb6e730ac6a975fc7652092af422b46e.png) The log file is just an empty file. I looked at the topics posted on here and double checked my metadata names matches the tree file , tried running it with a different environment using the `-use-conda` flag and updated the packages using `conda activate nextstrain conda update --all` Do you have any suggestions I could try? The error message as text ` augur refine --tree results/louisiana/tree\_raw.nwk --alignment results/louisiana/aligned.fasta --metadata results/combined\_metadata.tsv --output-tree results/louisiana/tree.nwk --output-node-data re sults/louisiana/branch\_lengths.json --root hCoV-19/Wuhan/Hu-1/2019 hCoV-19/Wuhan/WH01/2019 --timetree --clock-rate 0.0008 --clock-std-dev 0.0004 --coalescent skyline --date-inferenc e marginal --divergence-unit mutations --date-confidence --no-covariance --clock-filt er-iqd 4 2\>&1 | tee logs/refine\_louisiana.txt Activating conda environment: /home/evtlabuser/nextstrain/COVID/.snakemake/conda/4b3ea613 /bin/bash: line 1: 21239 Killed augur refine --tree results/louisiana/tree\_raw.nwk --alignment results/louisiana/ali gned.fasta --metadata results/combined\_metadata.tsv --output-tree results/louisiana/tree.nwk --output-node-data results/louisiana/bra nch\_lengths.json --root hCoV-19/Wuhan/Hu-1/2019 hCoV-19/Wuhan/WH01/2019 --timetree --clock-rate 0.0008 --clock-std-dev 0.0004 --coale scent skyline --date-inference marginal --divergence-unit mutations --date-confidence --no-covariance --clock-filter-iqd 4 2\>&1 21240 Done | tee logs/refine\_louisiana.txt [Thu Apr 8 18:17:42 2021] Error in rule refine: jobid: 4 output: results/louisiana/tree.nwk, results/louisiana/branch\_lengths.json log: logs/refine\_louisiana.txt (check log file(s) for error message) conda-env: /home/evtlabuser/nextstrain/COVID/.snakemake/conda/4b3ea613 shell: ``` augur refine --tree results/louisiana/tree_raw.nwk --alignment results/louisiana/aligned.fasta --metadata results/combined_metadata.tsv --output-tree results/louisiana/tree.nwk --output-node-data re sults/louisiana/branch_lengths.json --root hCoV-19/Wuhan/Hu-1/2019 hCoV-19/Wuhan/WH01/2019 --timetree --clock-rate 0.0008 --clock-std-dev 0.0004 --coalescent skyline --date-inferenc e marginal --divergence-unit mutations --date-confidence --no-covariance --clock-filt er-iqd 4 2>&1 | tee logs/refine_louisiana.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) ``` Logfile logs/refine\_louisiana.txt: Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message` ---
**Author:** ![MaartenVanDiest](https://avatars.discourse-cdn.com/v4/letter/m/76d3ee/32.png) [@MaartenVanDiest](https://nextstrain.discourse.group/u/MaartenVanDiest)\ **Post date:** [April 9, 2021, 6:58pm UTC](https://nextstrain.discourse.group/t/augur-refine-fails-but-does-not-generate-an-error-log/479/2 "2021-04-09T18:58:40Z")
The log files ![image](https://canada1.discourse-cdn.com/flex031/uploads/nextstrain/original/1X/0d9166ac1fd0a07ec2e7a8e17c37aa46f31dded4.png) ---
**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\ **Post date:** [April 9, 2021, 8:14pm UTC](https://nextstrain.discourse.group/t/augur-refine-fails-but-does-not-generate-an-error-log/479/3 "2021-04-09T20:14:29Z")
Hi @MaartenVanDiest, welcome! Sorry to hear you’re having trouble with your build. The tell-tale clue in the output you shared is: ```auto /bin/bash: line 1: 21239 Killed augur refine ``` This indicates that something, most likely your operating system, forcibly stopped the `augur refine` process (process id 21239), most likely because your system was experiencing an out-of-memory condition and started terminating processes to free up memory. How much memory is available to your workflow run? Our rough estimate for memory usage for the refine step of the workflow is about 15× the size on disk of the input MSA: > ---
**Author:** ![MaartenVanDiest](https://avatars.discourse-cdn.com/v4/letter/m/76d3ee/32.png) [@MaartenVanDiest](https://nextstrain.discourse.group/u/MaartenVanDiest)\ **Post date:** [April 9, 2021, 8:54pm UTC](https://nextstrain.discourse.group/t/augur-refine-fails-but-does-not-generate-an-error-log/479/4 "2021-04-09T20:54:38Z")
That’s a good to know. I have 2 GB available. I will have it extended to 16 GB to run properly and try again. Thanks for the help, Thomas! ---
**Author:** ![MaartenVanDiest](https://avatars.discourse-cdn.com/v4/letter/m/76d3ee/32.png) [@MaartenVanDiest](https://nextstrain.discourse.group/u/MaartenVanDiest)\ **Post date:** [April 12, 2021, 1:36pm UTC](https://nextstrain.discourse.group/t/augur-refine-fails-but-does-not-generate-an-error-log/479/5 "2021-04-12T13:36:30Z")
Extending the memory fixed all the issues.