IQTREE Error

[iqtree]

IQTREE Error

[roblanf]

Hi Bryan, This is something to do with the nextstrain snakemake workflow, and not iqtree. The right place to go for this is the nextstrain help/faq/github. The error is something straight from snakemake, so as far as I can see there is nothing we can help you with here from the IQ-TREE side. Rob

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On Thu, 7 Oct 2021 at 09:35, Bryan Tegomoh ***@***.***> wrote: Team, running into an iqtree error using iqtree in the nextstrain workflow. The error message looks like this: Waiting at most 30 seconds for missing files. MissingOutputException in line 750 of /mnt/c/Users/bryan/Documents/ncov/workflow/snakemake_rules/main_workflow.smk: Job Missing files after 30 seconds: results/Nebraska/nt_muts.json This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 38 completed successfully, but some output files are missing. 38 Not sure why this is happening. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#40>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG2SE6JSFKLROWYPAPEMF3UFTFLFANCNFSM5FP4QXXQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra www.robertlanfear.com

[tsibley]

Hi @roblanf, I'm from the Nextstrain team and was helping @BryanTegomoh out on our community forum. There's a little more context in the post over there, including the following screenshot which shows a segfault in IQ-TREE. The Snakemake error above is indeed from our workflow, but it's a downstream consequence of the segfault, not the underlying issue. Any insight into the segfault?

[roblanf]

Ah OK, that makes sense.

@bqminh can you shed any light here? @tsibley and @BryanTegomoh can you specify which version of IQ-TREE, and if possible (I know with COVID data it might not be possible) provide the input files and the log file.

[roblanf]

One thing I'd note in passing (I am almost certain this is completely unrelated to the issue you're having, which seems to be with computing distances), is that when using IQ-TREE on COVID data I'd recommend setting

-blmin 0.0000000000001

There are a lot of true zero length branches in most analyses. The default in IQ-TREE is to set -blmin to 0.1/alignment_length, which is about 0.00003, and that can have a pretty large effect on the likelihoods if the truth is zero.

[tsibley]

@roblanf Thanks for the tip about -blmin; I'll pass that along to the rest of the team.

As for IQ-TREE version, the version used in our workflow should be 2.1.2 from Bioconda. @BryanTegomoh also said he tested with 2.1.4_beta and 2.0.3 from Bioconda as well. I don't have input or log files, so @BryanTegomoh will have to supply those if possible.

[george-githinji]

In reference to the nextstrain/augur#780, I am getting the following error with IQ-Tree: This is happening with IQ-TREE multicore version 2.1.4-beta COVID-edition for Mac OS X 64-bit built Jun 24 2021

ERROR: Shell exited from fatal signal SIGSEGV when running: iqtree2 -ninit 2 -n 2 -me 0.05 -nt 10 -s results/filtered-delim.fasta -m GTR -ninit 10 -n 4 > results/filtered-delim.iqtree.log
Command output was:
  OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
  OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
  OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
  ERROR: STACK TRACE FOR DEBUGGING:
  ERROR: 2   _sigtramp()
  ERROR: 4   ModelSubst::computeTipLikelihood(unsigned int, double*)
  ERROR: 5   PhyloTree::computeTipPartialLikelihood()
  ERROR: 6   void PhyloTree::computeTraversalInfo<Vec4d, 4>(PhyloNode*, PhyloNode*, bool)
  ERROR: 7   double PhyloTree::computeLikelihoodBranchSIMD<Vec4d, true, 4, true, false>(PhyloNeighbor*, PhyloNode*)
  ERROR: 8   PhyloTree::optimizeAllBranches(int, double, int)
  ERROR: 9   IQTree::optimizeBranches(int)
  ERROR: 10   runTreeReconstruction(Params&, IQTree*&)
  ERROR: 11   runPhyloAnalysis(Params&, Checkpoint*)
  ERROR:
  ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
  ERROR: *** For bug report please send to developers:
  ERROR: ***    Log file: results/filtered-delim.fasta.log
  ERROR: ***    Alignment files (if possible)
  /bin/bash: line 1:  7615 Segmentation fault: 11  iqtree2 -ninit 2 -n 2 -me 0.05 -nt 10 -s results/filtered-delim.fasta -m GTR -ninit 10 -n 4 > results/filtered-delim.iqtree.log

Building a tree via:
	iqtree2 -ninit 2 -n 2 -me 0.05 -nt 10 -s results/filtered-delim.fasta -m GTR -ninit 10 -n 4 > results/filtered-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

ERROR: TREE BUILDING FAILED

[roblanf]

OK @bqminh and @JamesBarbetti, any thoughts on this?