ERROR: Numerical underflow (lh-branch)

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Chih-Wei Huang

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Jun 25, 2019, 9:40:49 AM6/25/19
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Hello, 
I'm try to use IQTREE web server for evaluating the best substitution model and partition scheme.
It was returned with an error message.

This job STOPPED because there was a problem!
WARNING: Too many iterations in tqli
WARNING: Too many iterations in tqli
WARNING: Too many iterations in tqli
ERROR: Numerical underflow (lh-branch). Run again with the safe likelihood kernel via `-safe` option

I couldn't figure out what the problem is.
Thanks for your help.

Best regards,
Chih-Wei


The following is the running log 

IQ-TREE multicore version 1.6.11 for Linux 64-bit built Jun  6 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    kronig (SSE4.2, 31 GB RAM)
Command: ../../iqtree -s 20190625_align_COIwithOG.fas -st DNA -sp COI_partition.txt -pre 20190625_align_COIwithOG.fas -m TESTONLYNEWMERGE
Seed:    351943 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Jun 25 15:39:17 2019
Kernel:  SSE2 - 1 threads (24 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 24 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading partition model file COI_partition.txt ...
Reading alignment file 20190625_align_COIwithOG.fas ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 150 sequences with 575 columns, 277 distinct patterns
253 parsimony-informative, 24 singleton sites, 298 constant sites
                                             Gap/Ambiguity  Composition  p-value
   1  B5                                             0.00%    passed     54.90%
   2  D3                                             0.00%    passed     54.90%
   3  VAL_00_Ea_Kar                                  0.00%    passed     36.91%
   4  VAR4                                           0.00%    passed     54.17%
   5  VAK_00_Xuyen_Moc                               0.00%    passed     62.54%
   .
   .
   .
147 OG_BRAI02 0.00% passed 83.99% 148 OG_BRNS01 0.00% failed 0.55% 149 ZY4 0.00% passed 13.50% 150 OG_J 0.00% failed 3.98% **** TOTAL 0.00% 2 sequences failed composition chi2 test (p-value<5%; df=3) Partition file is not in NEXUS format, assuming RAxML-style partition file... Subset Type Seqs Sites Infor Invar Model Name 1 DNA 150 192 191 0 GTR part1 2 DNA 150 192 48 133 GTR part2 3 DNA 150 191 14 165 GTR part3 Degree of missing data: 0.000 Info: multi-threading strategy over partitions NOTE: D3 is identical to B5 but kept for subsequent analysis NOTE: YD1 is identical to R50 but kept for subsequent analysis NOTE: YD7 is identical to YD2 but kept for subsequent analysis NOTE: YD8 is identical to YD4 but kept for subsequent analysis NOTE: XI3XI4XI6XI7XI8 is identical to XI0XI2 but kept for subsequent analysis NOTE: R31 is identical to R30 but kept for subsequent analysis NOTE: T71 is identical to T70 but kept for subsequent analysis NOTE: X61X62X63X64 is identical to X50-1-2-3-4-5-7 but kept for subsequent analysis NOTE: T30 is identical to T21 but kept for subsequent analysis NOTE: XA3567 is identical to XA1 but kept for subsequent analysis NOTE: VAY0 is identical to S51 but kept for subsequent analysis NOTE: VAO1 is identical to VAG_00_Chu_Prong but kept for subsequent analysis NOTE: XX6 is identical to XX0123457 but kept for subsequent analysis NOTE: T61 is identical to T60 but kept for subsequent analysis NOTE: X24 is identical to X21 but kept for subsequent analysis NOTE: XV0 is identical to X23 but kept for subsequent analysis NOTE: XH0XH2XH6789 is identical to XG1XG2XG8 but kept for subsequent analysis NOTE: XG4XG5 is identical to X22 but kept for subsequent analysis NOTE: XH4 is identical to XG7XG9 but kept for subsequent analysis NOTE: XV6 is identical to XG6 but kept for subsequent analysis NOTE: ZF9 is identical to ZE8 but kept for subsequent analysis NOTE: VAU1 is identical to T41 but kept for subsequent analysis NOTE: 16 identical sequences (see below) will be ignored for subsequent analysis NOTE: YD3 (identical to R50) is ignored but added at the end NOTE: YE4 (identical to R50) is ignored but added at the end NOTE: YE1 (identical to YD2) is ignored but added at the end NOTE: YE3 (identical to YD2) is ignored but added at the end NOTE: T31 (identical to T21) is ignored but added at the end NOTE: XW1XW3 (identical to XA1) is ignored but added at the end NOTE: VBA4 (identical to S51) is ignored but added at the end NOTE: T81 (identical to T60) is ignored but added at the end NOTE: X25 (identical to X21) is ignored but added at the end NOTE: XG0XG3 (identical to X21) is ignored but added at the end NOTE: XH1XH5 (identical to X21) is ignored but added at the end NOTE: XV3 (identical to X21) is ignored but added at the end NOTE: XV7 (identical to X21) is ignored but added at the end NOTE: XV2XV9 (identical to X23) is ignored but added at the end NOTE: XV5 (identical to XG1XG2XG8) is ignored but added at the end NOTE: XV1 (identical to XG7XG9) is ignored but added at the end Concatenated alignment was printed to 20190625_align_COIwithOG.fas.uniqueseq.phy For your convenience alignment with unique sequences printed to 20190625_align_COIwithOG.fas.uniqueseq.phy Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.018 seconds NOTE: ModelFinder requires 12 MB RAM! Testing GTR+F+G on supermatrix... GTR+F+G4 / LnL: -9241.935 / df: 274 / AIC: 19031.870 / AICc: 19534.204 / BIC: 20224.968 Selecting individual models for 3 charsets using BIC... No. Model Score Charset 1 TIM2+F+ASC+G4 14954.630 part1 WARNING: Too many iterations in tqli WARNING: Too many iterations in tqli WARNING: Too many iterations in tqli ERROR: Numerical underflow (lh-branch). Run again with the safe likelihood kernel via `-safe` option

Chih-Wei Huang

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Jun 25, 2019, 10:24:11 AM6/25/19
to IQ-TREE

I've try again. No error message.
Thanks!


Chih-Wei Huang於 2019年6月25日星期二 UTC+8下午9時40分49秒寫道:

Minh Bui

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Jun 25, 2019, 11:40:33 AM6/25/19
to iqt...@googlegroups.com, Chih-Wei Huang
Hi Chih-Wei,

Just as a head up: I saw that part1 has no invariant sites. This might or might not be problematic, but you should check the data carefully.

Cheers,
Minh

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