Error: For mixture model, you need to specify +F/+FO/+F{}/+FQ for every model

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Nanzhen

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Mar 9, 2023, 2:08:37 AM3/9/23
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Hey,

Does anyone know how to fix this problem?

I have been following the same protocol to build bacterial trees for a long time. I have no idea why it shows errors this time. Any help would be greatly appreciated!!

$ iqtree2 -s core_alignment.fasta -m TEST -alrt 1000 -bb 1000 -nt 8
IQ-TREE multicore version 2.2.0 COVID-edition for Linux 64-bit built Sep  1 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    gra705 (AVX2, FMA3, 125 GB RAM)
Command: core_alignment.fasta -m TEST -alrt 1000 -bb 1000 -nt 8
Seed:    867200 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Mar  9 02:01:15 2023
Kernel:  AVX+FMA - 8 threads (8 CPU cores detected)

Reading alignment file core_alignment.fasta ... Fasta format detected
Reading fasta file: done in 0.0719978 secs using 69.86% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.417143 secs using 49.7% CPU
Alignment has 11 sequences with 190956 columns, 75523 distinct patterns
70607 parsimony-informative, 51431 singleton sites, 68918 constant sites
                 Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.00726517 secs using 587.4% CPU
   1  GCF_0014340   0.51%    failed      0.00%
   2  GCF_0014360   0.76%    failed      0.00%
   3  GCF_001436   0.30%    failed      0.00%
   4  GCF_00143 0.87%    failed      0.00%
   5  GCF_02338   0.84%    failed      0.00%
   6  GCF_02402   0.07%    failed      0.00%
   7  GCF_02402    0.02%    failed      0.00%
   8  GCF_02402    0.03%    failed      0.00%
   9  GCF_0241    0.11%    failed      0.00%
  10  GCF_02402    1.71%    failed      0.00%
  11  GCF_024    0.17%    failed      0.00%
****  TOTAL              0.49%  11 sequences failed composition chi2 test (p-value<5%; df=19)
NOTE: minimal branch length is reduced to 0.000000523681 for long alignment
Checking for duplicate sequences: done in 0.00566472 secs using 438.3% CPU

NOTE: Restoring information from model checkpoint file core_alignment.fasta.model.gz

CHECKPOINT: Initial tree restored
ERROR: For mixture model, you need to specify +F/+FO/+F{}/+FQ for every model
ERROR: For example: MIX{GTR+FO,GTR+F}

Thanks!
Best,
Nanzhen

Thomas Wong

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Mar 9, 2023, 5:29:00 AM3/9/23
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Hi,

Can you try the version v2.2.2.3 (from https://github.com/iqtree/iqtree2/releases) and see whether the issue still exists? Thanks.

Thomas

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Aniket Ghosh

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Mar 9, 2023, 5:50:34 AM3/9/23
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Hi,
   Now I have used version v2.2.2.3 . Still, I am facing problems.

 IQ-TREE multicore version 2.2.2.3 COVID-edition for Windows 64-bit built Feb 25 2023

Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    DESKTOP-H8J1SD4 (AVX512, FMA3, 7 GB RAM)
Command: D:\Phylogeny _Software_AG\iqtree-2.2.2.3-Windows\iqtree-2.2.2.3-Windows\bin\iqtree2.exe -s Russula.fas -spp Partition.nex –m MF+MERGE -bb 1000
Seed:    937036 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Mar 09 16:17:42 2023
Kernel:  AVX+FMA - 1 threads (8 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading partition model file Partition.nex ...
Reading alignment file Russula.fas ... Fasta format detected
Reading fasta file: done in 0.0024748 secs
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.0042654 secs
Alignment has 58 sequences with 2191 columns, 705 distinct patterns
479 parsimony-informative, 89 singleton sites, 1622 constant sites
                                                       Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 9.49e-005 secs
   1  Multifurca_aurantiophylla_644_BB_09_119_New_Caledonia    4.70%    passed     49.18%
   2  Multifurca_ochricompacta_580_BB_07_010_USA               4.70%    passed     44.62%
   3  Russula_shoreae_Holotype_India1                          9.17%    passed     43.32%
   4  Russula_shoreae_India2                                   9.49%    passed     47.79%
   5  Russula_boddingii_Holotype_India1                        5.20%    passed     20.65%
   6  Russula_boddingii_India2                                 5.57%    passed     22.39%
   7  Russula_pseudoflavida_Holotype_India1                    6.62%    failed      0.54%
   8  Russula_pseudoflavida_India2                             6.94%    failed      0.43%
   9  Russula_aurata_547_BB_07_211_Slovakia                    7.71%    failed      1.15%
  10  Russula_luteotacta_452_BB_07_188_Europe                  4.43%    passed     23.18%
  11  Russula_persicina_428_BB_07_271_Europe                   5.66%    passed     22.32%
  12  Russula_gracillima_441_BB_07_785_Europe                  4.88%    passed     24.28%
  13  Russula_densifolia_439_BB_07_344_Slovakia                5.39%    passed     37.27%
  14  Russula_fuliginosa_1178_M_Floriani_Italy                 4.93%    passed     16.36%
  15  Russula_nigricans_429_BB_07_342_Slovakia                 7.58%    passed     32.57%
  16  Russula_adusta_223_BB_06_562_Canada                     10.09%    passed     36.74%
  17  Russula_acrifolia_543_BB_08_662_Italy                    5.93%    passed     32.63%
  18  Russula_zvarae_538_BB_08_639_Europe                      5.43%    passed     22.57%
  19  Russula_densifolia_RDL_16-001_2_Belgium                 29.07%    failed      3.70%
  20  Russula_densifolia_RDL_18-052_Belgium                   29.07%    failed      3.70%
  21  Russula_densifolia_RDL_17-024_Belgium                   29.07%    failed      3.70%
  22  Russula_cf_fuliginosa_FH_RUS_14091001_Slovakia          29.07%    failed      4.23%
  23  Russula_fuliginosa_FH_RUS_14091201_Slovakia             29.07%    failed      4.23%
  24  Russula_atramentosa_FH_2011-002R_Belgium                29.07%    passed     13.88%
  25  Russula_atramentosa_FH0170824-02_Germany                29.07%    passed     13.88%
  26  Russula_dissimulans_BPL285_USA                          30.76%    passed      5.24%
  27  Russula_nigricans_RDL_17-004_Belgium                    30.53%    failed      4.41%
  28  Russula_albonigra_JK_RUS_13090603_Germany               29.21%    failed      4.80%
  29  Russula_albonigra_SAV_F-20197_Slovakia                  29.16%    failed      4.46%
  30  Russula_nigrifacta_RDL_16-044_Italy                     29.16%    failed      3.72%
  31  Russula_peckii_BPL270_USA                               29.58%    passed     42.26%
  32  Russula_sardonia_FH12215_Germany                        29.53%    passed      7.13%
  33  Russula_sanguinea_FH12240_Germany                       29.71%    failed      2.40%
  34  Russula_queletii_FH12237_Germany                        30.21%    passed     15.78%
  35  Russula_redolens_BPL260_USA                             29.53%    failed      4.91%
  36  Russula_redolens_BPL141_USA                             29.53%    failed      4.46%
  37  Russula_cyanoxantha_FH_12-201_Germany                   30.40%    failed      2.67%
  38  Russula_cf_cyanoxantha_BPL280_USA                       29.53%    failed      3.12%
  39  Russula_cf_variata_BPL241_USA                           29.21%    failed      1.49%
  40  Russula_substriata_XHW4785_China                        28.94%    passed      7.05%
  41  Russula_maguanensis_XHW4765_China                       28.98%    passed     19.53%
  42  Russula_sp_GENT_FH_12-064_Thailand                      54.72%    failed      0.03%
  43  Russula_wielangtae_HO_593332_Australia                  56.32%    failed      0.02%
  44  Russula_velutipes_SAV_F-3428_Slovakia                   48.43%    failed      0.01%
  45  Russula_wielangtae_HO_593331_Australia                  77.91%    failed      0.00%
  46  Russula_densissima_FH_2014_ST04_Germany                 70.74%    passed     14.79%
  47  Russula_densissima_FH_2010_ST02_Germany                 70.74%    passed     14.79%
  48  Russula_subtilis_SAV_F-3805_USA                         77.32%    passed     59.96%
  49  Russula_phloginea_CNX530524304_China                    44.64%    passed     23.22%
  50  Russula_aurantioflava_LAH35410_Pakistan                 55.64%    failed      0.00%
  51  Russula_aurantioflava_LAH35405_Pakistan                 60.61%    failed      0.00%
  52  Russula_aurantioflava_LAH35408_Pakistan                 54.91%    failed      0.00%
  53  Russula_ambusta_SAV_F-3358_Slovakia                     58.42%    passed     18.51%
  54  Russula_cyanoxantha_UE29_09_2002-2_France               58.60%    passed     21.42%
  55  Russula_lotus_LF321_China                               58.51%    passed     15.49%
  56  Russula_inquinata_JAC9757_New_Zealand                   58.65%    passed     21.90%
  57  Russula_inquinata_JAC13249_New_Zealand                  58.65%    passed     25.28%
  58  Russula_inquinata_JAC11697_New_Zealand                  58.65%    passed     24.90%
WARNING: 15 sequences contain more than 50% gaps/ambiguity
****  TOTAL                                                   31.30%  25 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: No CharPartition defined, use all CharSets

Loading 5 partitions...
Identifying sites to remove: done in 0.0009624 secs
Identifying sites to remove: done in 0.000433 secs
Identifying sites to remove: done in 0.0003268 secs
Identifying sites to remove: done in 0.000237 secs
Identifying sites to remove: done in 0.0004619 secs
Subset Type Seqs Sites Infor Invar Model Name
1 51 945 166 750 part1
2 26 605 71 500 part2
3 47 214 34 169 part3
4 47 214 57 153 part4
5 47 213 151 51 part5
Degree of missing data: 0.260
Info: multi-threading strategy over partitions

NOTE: Russula_densifolia_RDL_18-052_Belgium is identical to Russula_densifolia_RDL_16-001_2_Belgium but kept for subsequent analysis
NOTE: Russula_fuliginosa_FH_RUS_14091201_Slovakia is identical to Russula_cf_fuliginosa_FH_RUS_14091001_Slovakia but kept for subsequent analysis
NOTE: Russula_atramentosa_FH0170824-02_Germany is identical to Russula_atramentosa_FH_2011-002R_Belgium but kept for subsequent analysis
NOTE: Russula_densissima_FH_2010_ST02_Germany is identical to Russula_densissima_FH_2014_ST04_Germany but kept for subsequent analysis
Identifying sites to remove: done in 0.0008692 secs
Identifying sites to remove: done in 0.000394 secs
Identifying sites to remove: done in 0.0001968 secs
Identifying sites to remove: done in 0.0002285 secs
Identifying sites to remove: done in 0.0004278 secs
NOTE: 1 identical sequences (see below) will be ignored for subsequent analysis
NOTE: Russula_densifolia_RDL_17-024_Belgium (identical to Russula_densifolia_RDL_16-001_2_Belgium) is ignored but added at the end
Alignment was printed to Partition.nex.uniqueseq.phy

For your convenience alignment with unique sequences printed to Partition.nex.uniqueseq.phy

Reading input tree file –m ...ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: Partition.nex.log
ERROR: ***    Alignment files (if possible)




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09/03/23, 16:20:16

Thomas Wong

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Mar 9, 2023, 6:23:39 AM3/9/23
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Hi,

Because you would like to do bootstrapping, you should use "MFP" instead of "MF".

MFP: "Find best partition scheme followed by tree inference and bootstrap"

That means your syntax should be: iqtree2.exe -s Russula.fas -spp Partition.nex –m MFP+MERGE -bb 1000

Thomas

Thomas Wong

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Mar 9, 2023, 6:43:29 AM3/9/23
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Hi Aniket,

By the way, when I copied and pasted your command, it didn't work. However, it worked when I typed the command again (exactly, but changed to MF to MFP). I guess there were some hidden characters.

Thomas

Aniket Ghosh

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Mar 9, 2023, 8:29:04 AM3/9/23
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Hi Thomas,
  Thank you very much for your suggestion. Now It works smoothly. 

Regards,
Aniket



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09/03/23, 18:56:48

Fabian Ruperti

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May 10, 2023, 9:57:07 AM5/10/23
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Hey everyone, 

I am facing a similar problem using IQ-TREE multicore version 2.2.0. 

With the following command, I get the following error:

iqtree2 -s MYLK_domains_MSA.fa -m MFP -B 1000 -alrt 1000 -abayes -nt AUTO

ERROR: For mixture model, you need to specify +F/+FO/+F{}/+FQ for every model
ERROR: For example: MIX{GTR+FO,GTR+F}

There are not hidden characters, etc. At least non that I can find. 

Thanks already for any help.
Regards, 
Fabian

Thomas Wong

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May 10, 2023, 7:35:26 PM5/10/23
to iqt...@googlegroups.com, Fabian Ruperti

Hi Fabian,

The issue should have been addressed in the later version. Can you try the latest version, say v2.2.2.5, at https://github.com/iqtree/iqtree2/releases ?

Thomas

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