[BUG] Error building tree using example data

Hi, I’m trying to run a SARS-CoV-2 analysis using the example data with 418 sequences using the default command snakemake --profile profiles/default. 48% of the steps finish successfully, however, I get an error in building the tree as follows: ERROR: b"ERROR: alignment.cpp:75: std::__cxx11::string& Alignment::getSeqName(int): Assertion `i >= 0 && i < (int)seq_names.size()’ failed.\nERROR: STACK TRACE FOR DEBUGGING:\nERROR: 1 funcAbort()\nERROR: 2 ()\nERROR: 3 gsignal()\nERROR: 4 abort()\nERROR: 5 ()\nERROR: 6 ()\nERROR: 7 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 8 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 9 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 10 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 11 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 12 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 13 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 14 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 15 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 16 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 17 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 18 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 19 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 20 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 21 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 22 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 23 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 24 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 25 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 26 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 27 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 28 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 29 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 30 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 31 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 32 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 33 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 34 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 35 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 36 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 37 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 38 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 39 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 40 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 41 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 42 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 43 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 44 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 45 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 46 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 47 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 48 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 49 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 50 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 51 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 52 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 53 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 54 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 55 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 56 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 57 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 58 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 59 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 60 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 61 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 62 PhyloTree::assignLeafNames(Node*, Node*)\nERROR: 63 PhyloTree::readTreeString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)\nERROR: \nERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED\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: 5995 Aborted (core dumped) iqtree -ninit 2 -n 2 -me 0.05 -nt 2 -s results/global/subsampled_alignment-delim.fasta -m GTR -ninit 10 -n 4 > results/global/subsampled_alignment-delim.iqtree.log\n" shell exited 134 when running: iqtree -ninit 2 -n 2 -me 0.05 -nt 2 -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 2 -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

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

Building original tree took 4.321278810501099 seconds [Mon Jun 8 02:37:36 2020] Error in rule tree: jobid: 15 output: results/global/tree_raw.nwk log: logs/tree_global.txt (check log file(s) for error message) shell:

    augur tree             --alignment results/global/subsampled_alignment.fasta             --tree-builder-args '-ninit 10 -n 4'             --output results/global/tree_raw.nwk             --nthreads 2 2>&1 | tee logs/tree_global.txt
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/vs/Downloads/COVID_Research/ncov/.snakemake/log/2020-06-08T023515.929219.snakemake.log

Could you help with this? I’ve not modified anything, I’m just using the files given and the default command.

[pvanheus]

Hi there - I know this is a closed issued but I hit the same error. This post on the Iqtree forum discusses this issue. As Dr Bui states: “It means that you had a previous (unfinished) run and IQ-TREE loaded the checkpoint file. From what you wrote below, I’m guessing that you now change the alignment file (-s option). This causes incompability between the checkpoint and the alignment.”

This does, I think, describe the circumstances in which I encountered this: I had started a Nextstrain build, then terminated it for some reason, added some more sequences to the input data and re-started the build. I can imagine some “checkpoint” file being left behind in the results directory that contracted the alignment file. I subsequently deleted the results directory and re-started the build. It has now proceeded past the tree-building step with no errors.

I haven’t been able to prove that this is the source of the error but I’m just leaving this theory here for further investigation…

[trvrb]

I’m closing this issue now. @Addicted-to-coding please let us know if you’re still running into this problem with the latest version of ncov and we can reopen if it’s still a problem.