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