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Best-fit model selection
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`next_block < bin_header.max_blocks` failed #10

Open widdowquinn opened 6 years ago

widdowquinn commented 6 years ago

Using modeltest-ng v0.1.2 static 64bit Linux binary (downloaded from releases at GitHub), running on:

$ uname -a
Linux <MACHINE_NAME> 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

with the command:

$ modeltest-ng/modeltest-ng -T raxml -i PF14200/nt_backtrans.trimal.1.fasta

and the attached data: nt_backtrans.trimal.1.fasta.txt (.txt extension only to get GitHub to allow upload)

I see the error:

Partition 1/1

    1/24   JC             0h:00:00   0h:00:01           -4488.8506       -       -
    2/24   JC+I           0h:00:00   0h:00:01           -4466.1916       -  0.0208
    3/24   JC+G           0h:00:00   0h:00:01           -4366.1397  1.6524       -
    4/24   JC+I+G         0h:00:00   0h:00:01           -4363.1826  1.9105  0.0200
    5/24   F81            0h:00:00   0h:00:01           -4486.9120       -       -
    6/24   F81+I          0h:00:00   0h:00:01           -4462.7894       -  0.0208
    7/24   F81+G          0h:00:00   0h:00:01           -4355.4930  1.5209       -
    8/24   F81+I+G        0h:00:00   0h:00:01           -4352.1043  1.7593  0.0200
    9/24   K80            0h:00:00   0h:00:01           -4471.1617       -       -
   10/24   K80+I          0h:00:00   0h:00:01           -4448.2561       -  0.0208
modeltest-ng: binary_io_operations.c:109: binary_update_header: Assertion `next_block < bin_header.max_blocks' failed.

but I don't understand the reason for failure. With the verbose flag, the error reported is:

Partition 1/1

    1/24   JC             0h:00:00   0h:00:01           -4488.8506       -       -
    2/24   JC+I           0h:00:00   0h:00:01           -4466.1916       -  0.0208
    3/24   JC+G           0h:00:00   0h:00:01           -4366.1397  1.6524       -
    4/24   JC+I+G         0h:00:00   0h:00:01           -4363.1826  1.9105  0.0200
    5/24   F81            0h:00:00   0h:00:01           -4486.9120       -       -
    6/24   F81+I          0h:00:00   0h:00:01           -4462.7894       -  0.0208
    7/24   F81+G          0h:00:00   0h:00:01           -4355.4930  1.5209       -
    8/24   F81+I+G        0h:00:00   0h:00:01           -4352.1043  1.7593  0.0200
    9/24   K80            0h:00:00   0h:00:01           -4471.1617       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial log likelihood: -4917.97
[dbg] final parameter optimization: -4917.97
[dbg] fix branches -4499.17
[dbg] optimize BranchLengths: -4499.17
[dbg] optimize P-inv: -4499.17
[dbg] optimize Frequencies: -4499.17
[dbg] optimize Alpha: -4499.17
[dbg] optimize SubstRates: -4450.49
[dbg] fix branches -4448.38
[dbg] optimize BranchLengths: -4448.38
[dbg] optimize P-inv: -4448.38
[dbg] optimize Frequencies: -4448.38
[dbg] optimize Alpha: -4448.38
[dbg] optimize SubstRates: -4448.33
[dbg] fix branches -4448.26
[dbg] optimize BranchLengths: -4448.26
[dbg] optimize P-inv: -4448.26
[dbg] optimize Frequencies: -4448.26
[dbg] optimize Alpha: -4448.26
[dbg] optimize SubstRates: -4448.26
[dbg] fix branches -4448.26
[dbg] optimize BranchLengths: -4448.26
[dbg] optimize P-inv: -4448.26
[dbg] optimize Frequencies: -4448.26
[dbg] optimize Alpha: -4448.26
[dbg] optimize SubstRates: -4448.26
[dbg] model done: [0.01/0.0001]: -4448.26
[dbg] Model optimization done: -4448.26
   10/24   K80+I          0h:00:00   0h:00:01           -4448.2561       -  0.0208
modeltest-ng: binary_io_operations.c:109: binary_update_header: Assertion `next_block < bin_header.max_blocks' failed.
Aborted (core dumped)

Thank you in advance for your help.

L.

widdowquinn commented 6 years ago

It may not help much, but I see the same result on this data using the v0.1.1 Linux pre-built binary, though not with the precompiled v0.1.1 GUI on OSX.

ddarriba commented 6 years ago

Thank you very much for the report, Leighton.

Sorry for the late reply. It seems there was a bug affecting the consistency between the model optimization and the checkpointing. I fixed that in the dev branch, and I will add a new release soon. Meanwhile, it is possible to evaluate RAxML models with "-m JC,HKY,GTR -f e" arguments.

Best, Diego.

ealdraed commented 5 years ago

Hello Diego (@ddarriba),

I am using ModelTest-NG 0.1.5 (precompiled modeltest-ng-0.1.5 static linux64 from this repository) and encounter the same failure. I will give you a minimal example FASTA file (only three sequences):

MinExample.fasta.txt (remove .txt)

./modeltest-ng -i MinExample.fasta -s 203 -v

[...]

Partition 1/1

[dbg] ... ... build partition optimizer 
[dbg] ... ... evaluate partition
Step 1/6
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11496.6
[dbg] Initial log likelihood: -11496.6
[dbg] final parameter optimization: -11496.6
[dbg] fix branches -9575.44
[dbg] optimize BranchLengths: -9575.44
[dbg] optimize FixedFrequencies: -9575.44
[dbg] optimize Alpha: -9575.44
[dbg] optimize SubstRates: -9575.03
[dbg] fix branches -9575.03
[dbg] optimize BranchLengths: -9575.03
[dbg] optimize FixedFrequencies: -9575.03
[dbg] optimize Alpha: -9575.03
[dbg] optimize SubstRates: -9575.03
[dbg] model done: [0.01/0.01]: -9575.03
[dbg] Model optimization done: -9575.03
    1/8    SYM            0h:00:00   0h:00:00           -9575.0307       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11136.1
[dbg] Initial log likelihood: -11136.1
[dbg] final parameter optimization: -11136.1
[dbg] fix branches -9575.44
[dbg] optimize BranchLengths: -9575.44
[dbg] optimize P-inv: -9575.44
[dbg] optimize FixedFrequencies: -9575.44
[dbg] optimize Alpha: -9575.44
[dbg] optimize SubstRates: -9575.03
[dbg] fix branches -9575.03
[dbg] optimize BranchLengths: -9575.03
[dbg] optimize P-inv: -9575.03
[dbg] optimize FixedFrequencies: -9575.03
[dbg] optimize Alpha: -9575.03
[dbg] optimize SubstRates: -9575.03
[dbg] model done: [0.01/0.01]: -9575.03
[dbg] Model optimization done: -9575.03
    2/8    SYM+I          0h:00:00   0h:00:04           -9575.0309       -  0.0204
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11259.1
[dbg] Initial log likelihood: -11259.1
[dbg] final parameter optimization: -11259.1
[dbg] fix branches -9575.44
[dbg] optimize BranchLengths: -9575.44
[dbg] optimize FixedFrequencies: -9575.44
[dbg] optimize Alpha: -9575.44
[dbg] optimize SubstRates: -9575.03
[dbg] fix branches -9575.03
[dbg] optimize BranchLengths: -9575.03
[dbg] optimize FixedFrequencies: -9575.03
[dbg] optimize Alpha: -9575.03
[dbg] optimize SubstRates: -9575.03
[dbg] model done: [0.01/0.01]: -9575.03
[dbg] Model optimization done: -9575.03
    3/8    SYM+G4         0h:00:00   0h:00:04           -9575.0308 98.3752       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -10856.8
[dbg] Initial log likelihood: -10856.8
[dbg] final parameter optimization: -10856.8
[dbg] fix branches -9575.44
[dbg] optimize BranchLengths: -9575.44
[dbg] optimize P-inv: -9575.44
[dbg] optimize FixedFrequencies: -9575.44
[dbg] optimize Alpha: -9575.44
[dbg] optimize SubstRates: -9575.03
[dbg] fix branches -9575.03
[dbg] optimize BranchLengths: -9575.03
[dbg] optimize P-inv: -9575.03
[dbg] optimize FixedFrequencies: -9575.03
[dbg] optimize Alpha: -9575.03
[dbg] optimize SubstRates: -9575.03
[dbg] model done: [0.01/0.01]: -9575.03
[dbg] Model optimization done: -9575.03
    4/8    SYM+I+G4       0h:00:00   0h:00:04           -9575.0311 98.3752  0.0204
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11517.8
[dbg] Initial log likelihood: -11517.8
[dbg] final parameter optimization: -11517.8
[dbg] fix branches -9559.32
[dbg] optimize BranchLengths: -9559.32
[dbg] optimize OptFrequencies: -9559.32
[dbg] optimize Alpha: -9559.32
[dbg] optimize SubstRates: -9558.89
[dbg] fix branches -9558.89
[dbg] optimize BranchLengths: -9558.89
[dbg] optimize OptFrequencies: -9558.89
[dbg] optimize Alpha: -9558.89
[dbg] optimize SubstRates: -9558.89
[dbg] model done: [0.01/0.01]: -9558.89
[dbg] Model optimization done: -9558.89
    5/8    GTR            0h:00:00   0h:00:04           -9558.8884       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11138.5
[dbg] Initial log likelihood: -11138.5
[dbg] final parameter optimization: -11138.5
[dbg] fix branches -9559.32
[dbg] optimize BranchLengths: -9559.32
[dbg] optimize P-inv: -9559.32
[dbg] optimize OptFrequencies: -9559.32
[dbg] optimize Alpha: -9559.32
[dbg] optimize SubstRates: -9558.89
[dbg] fix branches -9558.89
[dbg] optimize BranchLengths: -9558.89
[dbg] optimize P-inv: -9558.89
[dbg] optimize OptFrequencies: -9558.89
[dbg] optimize Alpha: -9558.89
[dbg] optimize SubstRates: -9558.89
[dbg] model done: [0.01/0.01]: -9558.89
[dbg] Model optimization done: -9558.89
    6/8    GTR+I          0h:00:00   0h:00:04           -9558.8885       -  0.0204
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11268.5
[dbg] Initial log likelihood: -11268.5
[dbg] final parameter optimization: -11268.5
[dbg] fix branches -9559.32
[dbg] optimize BranchLengths: -9559.32
[dbg] optimize OptFrequencies: -9559.32
[dbg] optimize Alpha: -9559.32
[dbg] optimize SubstRates: -9558.89
[dbg] fix branches -9558.89
[dbg] optimize BranchLengths: -9558.89
[dbg] optimize OptFrequencies: -9558.89
[dbg] optimize Alpha: -9558.89
[dbg] optimize SubstRates: -9558.89
[dbg] model done: [0.01/0.01]: -9558.89
[dbg] Model optimization done: -9558.89
    7/8    GTR+G4         0h:00:00   0h:00:04           -9558.8885 98.3752       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -10851.9
[dbg] Initial log likelihood: -10851.9
[dbg] final parameter optimization: -10851.9
[dbg] fix branches -9559.32
[dbg] optimize BranchLengths: -9559.32
[dbg] optimize P-inv: -9559.32
[dbg] optimize OptFrequencies: -9559.32
[dbg] optimize Alpha: -9559.32
[dbg] optimize SubstRates: -9558.89
[dbg] fix branches -9558.89
[dbg] optimize BranchLengths: -9558.89
[dbg] optimize P-inv: -9558.89
[dbg] optimize OptFrequencies: -9558.89
[dbg] optimize Alpha: -9558.89
[dbg] optimize SubstRates: -9558.89
[dbg] model done: [0.01/0.01]: -9558.89
[dbg] Model optimization done: -9558.89
    8/8    GTR+I+G4       0h:00:00   0h:00:04           -9558.8887 98.3752  0.0204
Step 2/6
[dbg] Attempting to load partition from checkpoint MinExample.fasta.ckp
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11518.4
[dbg] Initial log likelihood: -11518.4
[dbg] final parameter optimization: -11518.4
[dbg] fix branches -9575.99
[dbg] optimize BranchLengths: -9575.99
[dbg] optimize FixedFrequencies: -9575.99
[dbg] optimize Alpha: -9575.99
[dbg] optimize SubstRates: -9575.65
[dbg] fix branches -9575.65
[dbg] optimize BranchLengths: -9575.65
[dbg] optimize FixedFrequencies: -9575.65
[dbg] optimize Alpha: -9575.65
[dbg] optimize SubstRates: -9575.65
[dbg] model done: [0.01/0.01]: -9575.65
[dbg] Model optimization done: -9575.65
    1/120  001234         0h:00:00   0h:00:04           -9575.6464       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11528.4
[dbg] Initial log likelihood: -11528.4
[dbg] final parameter optimization: -11528.4
[dbg] fix branches -9559.9
[dbg] optimize BranchLengths: -9559.9
[dbg] optimize OptFrequencies: -9559.9
[dbg] optimize Alpha: -9559.9
[dbg] optimize SubstRates: -9559.52
[dbg] fix branches -9559.52
[dbg] optimize BranchLengths: -9559.52
[dbg] optimize OptFrequencies: -9559.52
[dbg] optimize Alpha: -9559.52
[dbg] optimize SubstRates: -9559.52
[dbg] model done: [0.01/0.01]: -9559.52
[dbg] Model optimization done: -9559.52
    2/120  001234[F]      0h:00:00   0h:00:04           -9559.5240       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11496.6
[dbg] Initial log likelihood: -11496.6
[dbg] final parameter optimization: -11496.6
[dbg] fix branches -9575.44
[dbg] optimize BranchLengths: -9575.44
[dbg] optimize FixedFrequencies: -9575.44
[dbg] optimize Alpha: -9575.44
[dbg] optimize SubstRates: -9575
[dbg] fix branches -9575
[dbg] optimize BranchLengths: -9575
[dbg] optimize FixedFrequencies: -9575
[dbg] optimize Alpha: -9575
[dbg] optimize SubstRates: -9575
[dbg] model done: [0.01/0.01]: -9575
[dbg] Model optimization done: -9575
    3/120  010234         0h:00:00   0h:00:04           -9575.0042       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11517.8
[dbg] Initial log likelihood: -11517.8
[dbg] final parameter optimization: -11517.8
[dbg] fix branches -9559.32
[dbg] optimize BranchLengths: -9559.32
[dbg] optimize OptFrequencies: -9559.32
[dbg] optimize Alpha: -9559.32
[dbg] optimize SubstRates: -9558.88
[dbg] fix branches -9558.88
[dbg] optimize BranchLengths: -9558.88
[dbg] optimize OptFrequencies: -9558.88
[dbg] optimize Alpha: -9558.88
[dbg] optimize SubstRates: -9558.88
[dbg] model done: [0.01/0.01]: -9558.88
[dbg] Model optimization done: -9558.88
    4/120  010234[F]      0h:00:00   0h:00:04           -9558.8763       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11508.3
[dbg] Initial log likelihood: -11508.3
[dbg] final parameter optimization: -11508.3
[dbg] fix branches -9576.14
[dbg] optimize BranchLengths: -9576.14
[dbg] optimize FixedFrequencies: -9576.14
[dbg] optimize Alpha: -9576.14
[dbg] optimize SubstRates: -9575.77
[dbg] fix branches -9575.77
[dbg] optimize BranchLengths: -9575.77
[dbg] optimize FixedFrequencies: -9575.77
[dbg] optimize Alpha: -9575.77
[dbg] optimize SubstRates: -9575.77
[dbg] model done: [0.01/0.01]: -9575.77
[dbg] Model optimization done: -9575.77
    5/120  012034         0h:00:00   0h:00:04           -9575.7733       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11522
[dbg] Initial log likelihood: -11522
[dbg] final parameter optimization: -11522
[dbg] fix branches -9560.06
[dbg] optimize BranchLengths: -9560.06
[dbg] optimize OptFrequencies: -9560.06
[dbg] optimize Alpha: -9560.06
[dbg] optimize SubstRates: -9559.67
[dbg] fix branches -9559.67
[dbg] optimize BranchLengths: -9559.67
[dbg] optimize OptFrequencies: -9559.67
[dbg] optimize Alpha: -9559.67
[dbg] optimize SubstRates: -9559.67
[dbg] model done: [0.01/0.01]: -9559.67
[dbg] Model optimization done: -9559.67
    6/120  012034[F]      0h:00:00   0h:00:04           -9559.6698       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11496.6
[dbg] Initial log likelihood: -11496.6
[dbg] final parameter optimization: -11496.6
[dbg] fix branches -9575.44
[dbg] optimize BranchLengths: -9575.44
[dbg] optimize FixedFrequencies: -9575.44
[dbg] optimize Alpha: -9575.44
[dbg] optimize SubstRates: -9575.03
[dbg] fix branches -9575.03
[dbg] optimize BranchLengths: -9575.03
[dbg] optimize FixedFrequencies: -9575.03
[dbg] optimize Alpha: -9575.03
[dbg] optimize SubstRates: -9575.03
[dbg] model done: [0.01/0.01]: -9575.03
[dbg] Model optimization done: -9575.03
    7/120  012304         0h:00:00   0h:00:04           -9575.0343       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11517.8
[dbg] Initial log likelihood: -11517.8
[dbg] final parameter optimization: -11517.8
[dbg] fix branches -9559.32
[dbg] optimize BranchLengths: -9559.32
[dbg] optimize OptFrequencies: -9559.32
[dbg] optimize Alpha: -9559.32
[dbg] optimize SubstRates: -9558.88
[dbg] fix branches -9558.88
[dbg] optimize BranchLengths: -9558.88
[dbg] optimize OptFrequencies: -9558.88
[dbg] optimize Alpha: -9558.88
[dbg] optimize SubstRates: -9558.88
[dbg] model done: [0.01/0.01]: -9558.88
[dbg] Model optimization done: -9558.88
    8/120  012304[F]      0h:00:00   0h:00:04           -9558.8849       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial score: -11482.3
[dbg] Initial log likelihood: -11482.3
[dbg] final parameter optimization: -11482.3
[dbg] fix branches -9575.91
[dbg] optimize BranchLengths: -9575.91
[dbg] optimize FixedFrequencies: -9575.91
[dbg] optimize Alpha: -9575.91
[dbg] optimize SubstRates: -9575.63
[dbg] fix branches -9575.63
[dbg] optimize BranchLengths: -9575.63
[dbg] optimize FixedFrequencies: -9575.63
[dbg] optimize Alpha: -9575.63
[dbg] optimize SubstRates: -9575.63
[dbg] model done: [0.01/0.01]: -9575.63
[dbg] Model optimization done: -9575.63
    9/120  012340         0h:00:00   0h:00:04           -9575.6345       -       -
modeltest-ng: binary_io_operations.c:109: binary_update_header: Assertion `next_block < bin_header.max_blocks' failed.
Aborted (core dumped)

If I add --disable-checkpoint to the command, the program will finish without problems. So I guess it is also related to the checkpointing.

Setramis commented 3 years ago

hello everybody

I had the same problem usign the command line:

modeltest-ng -i my_aligment.fasta -p 8 -d nt -t ml -h uigf -f ef -s 11 -o my_data.modeltest-ng.txt

It was running for 3 hours, and then give me the error: _modeltest-ng: /home/modeltest-ng-0.1.7/libs/pll-modules/src/binary/binary_io_operations.c:109: binary_update_header: Assertion `next_block < bin_header.maxblocks' failed. Aborted (core dumped)

My data consisted of 5 hundred samples of 14k bp length.

Finally, i just skipped the -t ml option, and then the program finished successfully, in less than 2 minutes.