Open widdowquinn opened 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.
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.
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.
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.
Using
modeltest-ng
v0.1.2 static 64bit Linux binary (downloaded fromreleases
at GitHub), running on:with the command:
and the attached data: nt_backtrans.trimal.1.fasta.txt (
.txt
extension only to get GitHub to allow upload)I see the error:
but I don't understand the reason for failure. With the verbose flag, the error reported is:
Thank you in advance for your help.
L.