# Error: tree building failed

**URL:** <https://nextstrain.discourse.group/t/error-tree-building-failed/268>\
**Category:** Help and Getting Started\
**Created:** [January 7, 2021, 5:22am UTC](https://nextstrain.discourse.group/t/error-tree-building-failed/268 "2021-01-07T05:22:09Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Yan](https://avatars.discourse-cdn.com/v4/letter/y/3e96dc/32.png) [@Yan](https://nextstrain.discourse.group/u/Yan)\
**Post date:** [January 7, 2021, 5:22am UTC](https://nextstrain.discourse.group/t/error-tree-building-failed/268/1 "2021-01-07T05:22:09Z")

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Hello, I am a new for nextstrain. I have the problem when I follow the tutorial. I appreciate if you give me some suggestion. Thank you.

Here is logs/tree\_global.txt  
ERROR: b’ERROR: \nERROR: \*\*\* IQ-TREE CRASHES WITH SIGNAL ILLEGAL INSTRUCTION\nERROR: \*\*\* For bug report please send to developers:\nERROR: \*\*\* Log file: results/global/subsampled\_alignment-delim.fasta.log\nERROR: \*\*\* Alignment files (if possible)\n/bin/bash: line 1: 35314 Illegal instruction: 4 iqtree -ninit 2 -n 2 -me 0.05 -nt 4 -s results/global/subsampled\_alignment-delim.fasta -m GTR -ninit 10 -n 4 \> results/global/subsampled\_alignment-delim.iqtree.log\n’  
shell exited 132 when running: iqtree -ninit 2 -n 2 -me 0.05 -nt 4 -s results/global/subsampled\_alignment-delim.fasta -m GTR -ninit 10 -n 4 \> results/global/subsampled\_alignment-delim.iqtree.log

Building a tree via:  
iqtree -ninit 2 -n 2 -me 0.05 -nt 4 -s results/global/subsampled\_alignment-delim.fasta -m GTR -ninit 10 -n 4 \> results/global/subsampled\_alignment-delim.iqtree.log  
Nguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.  
Mol. Biol. Evol., 32:268-274. [https://doi.org/10.1093/molbev/msu300](https://doi.org/10.1093/molbev/msu300)

ERROR: TREE BUILDING FAILED  
Please see the log file for more details: results/global/subsampled\_alignment-delim.iqtree.log

Building original tree took 2.101897954940796 seconds

Thank you.  
Yan

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**Author:** ![Yan](https://avatars.discourse-cdn.com/v4/letter/y/3e96dc/32.png) [@Yan](https://nextstrain.discourse.group/u/Yan)\
**Post date:** [January 7, 2021, 9:01pm UTC](https://nextstrain.discourse.group/t/error-tree-building-failed/268/2 "2021-01-07T21:01:43Z")

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Hi I am still waiting the answers,  
I find more information about error, maybe useful, thanks.

\*\*\*\* TOTAL 1.10% 0 sequences failed composition chi2 test (p-value\<5%; df=3)  
NOTE: France\_DELIM-MQNWQTYYSCTNUJKVNVAA\_10060KV\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 is identical to Wuhan\_DELIM-MQNWQTYYSCTNUJKVNVAA\_Hu-1\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2019 but kept for subsequent analysis  
NOTE: USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_CA-CZB-1097\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 is identical to ENV\_DELIM-MQNWQTYYSCTNUJKVNVAA\_USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_UF-11\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 but kept for subsequent analysis  
NOTE: France\_DELIM-MQNWQTYYSCTNUJKVNVAA\_10078MA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 is identical to France\_DELIM-MQNWQTYYSCTNUJKVNVAA\_10006HC\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 but kept for subsequent analysis  
NOTE: France\_DELIM-MQNWQTYYSCTNUJKVNVAA\_40003KA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 is identical to France\_DELIM-MQNWQTYYSCTNUJKVNVAA\_10015BY\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 but kept for subsequent analysis  
NOTE: Greece\_DELIM-MQNWQTYYSCTNUJKVNVAA\_259\_31928\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 is identical to Greece\_DELIM-MQNWQTYYSCTNUJKVNVAA\_139\_32716\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 but kept for subsequent analysis  
NOTE: USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_CA-CZB-1085\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 is identical to USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_CA-CZB-1045\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 but kept for subsequent analysis  
NOTE: 3 identical sequences (see below) will be ignored for subsequent analysis  
NOTE: USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_VA-DCLS-0018\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 (identical to ENV\_DELIM-MQNWQTYYSCTNUJKVNVAA\_USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_UF-11\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020) is ignored but added at the end  
NOTE: USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_WA4-UW2\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 (identical to ENV\_DELIM-MQNWQTYYSCTNUJKVNVAA\_USA\_DELIM-MQNWQTYYSCTNUJKVNVAA\_UF-11\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020) is ignored but added at the end  
NOTE: Greece\_DELIM-MQNWQTYYSCTNUJKVNVAA\_37\_35684\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020 (identical to Greece\_DELIM-MQNWQTYYSCTNUJKVNVAA\_139\_32716\_DELIM-MQNWQTYYSCTNUJKVNVAA\_2020) is ignored but added at the end

For your convenience alignment with unique sequences printed to results/global/subsampled\_alignment-delim.fasta.uniqueseq.phy

Create initial parsimony tree by phylogenetic likelihood library (PLL)… 0.011 seconds

NOTE: 5 MB RAM (0 GB) is required!  
Estimate model parameters (epsilon = 0.500)

1. Initial log-likelihood: -43876.481  
ERROR:  
ERROR: \*\*\* IQ-TREE CRASHES WITH SIGNAL ILLEGAL INSTRUCTION  
ERROR: \*\*\* For bug report please send to developers:  
ERROR: \*\*\* Log file: results/global/subsampled\_alignment-delim.fasta.log  
ERROR: \*\*\* Alignment files (if possible)

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<div class="post-metadata">

**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:** [January 9, 2021, 12:56am UTC](https://nextstrain.discourse.group/t/error-tree-building-failed/268/3 "2021-01-09T00:56:26Z")

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Hi, @Yan, welcome!

> [@Yan](#):
>
> ERROR: \*\*\* IQ-TREE CRASHES WITH SIGNAL ILLEGAL INSTRUCTION  
> ERROR: \*\*\* For bug report please send to developers:  
> ERROR: \*\*\* Log file: results/global/subsampled\_alignment-delim.fasta.log  
> ERROR: \*\*\* Alignment files (if possible)

Unfortunately, this appears to be a bug in IQ-TREE itself, not Augur or Nextstrain’s usage of it. I would suggest doing what the error message suggests and filing a bug report with the IQ-TREE developers (including the log + alignment files).

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**Author:** ![Dana](https://avatars.discourse-cdn.com/v4/letter/d/9de053/32.png) [@Dana](https://nextstrain.discourse.group/u/Dana)\
**Post date:** [March 15, 2021, 10:01am UTC](https://nextstrain.discourse.group/t/error-tree-building-failed/268/4 "2021-03-15T10:01:58Z")

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If it helps I received a similar error and it turned out that storage was full.

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<div class="post-metadata">

**Author:** ![Yan](https://avatars.discourse-cdn.com/v4/letter/y/3e96dc/32.png) [@Yan](https://nextstrain.discourse.group/u/Yan)\
**Post date:** [March 15, 2021, 8:23pm UTC](https://nextstrain.discourse.group/t/error-tree-building-failed/268/5 "2021-03-15T20:23:47Z")

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Hi Dana, thank you so much for your suggestion. I am still waiting IQtree team reply until now. But I don’t think it is my storage problem. My mac is new, and no more app installed currently, so the other software don’t occupied many RAM. And I don’t use VM to run this, I directly run on python. Even I tried the small set of samples, I still get the same error.

I feel maybe some connection between IQtree and Nextstrain missing,  
My question is still here in IQTREE, and I attached the log file in it.

> <https://github.com/Cibiv/IQ-TREE/issues/184>
>
> subsampled\_alignment-delim.fasta.log
> tree\_global.txt
> Hello. I put my error on the Nextstrain website, after the system admin checked my error log, they gave me the...

Thank you for all suggestion.  
Yan