RAxML-NG 1.0.1 bootstrap: "terminate called recursively"

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Nicolás Peñafiel

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Sep 20, 2021, 2:55:44 PMSep 20
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Dear community:

I have been having an issue when running bootstrap for my tree. 
After starting, at some, sooner or later the job ends with the message: "terminate called recursively" in the scheduler's log file.

The code I used is:
#SBATCH --cpus-per-task=8
#SBATCH --mem=1G

module load StdEnv/2020  gcc/9.3.0  openmpi/4.0.3  raxml-ng/1.0.1
export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"

raxml-ng --bootstrap --msa TVM.raxml.rba --model TVM+I+G4  --seed 5 --threads ${OMP_NUM_THREADS} --prefix TVM_BS_2 --bs-trees 5000


I had previously determined the best model using Modeltest. The job doesn't end due to a lack of time or memory. 

I am attaching the raxml's log file, the scheduler log file and the MSA.

Your help is appreciated.

Nicolas

TVM.raxml.rba
TVM_BS_2.raxml.log
slurm-13986840.out

Nicolás Peñafiel

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Sep 22, 2021, 12:04:35 PMSep 22
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Hi again. 

I tried running the bootstrap for that MSA again (with a different seed and prefix) and again it stopped after 56 replicates, only that a new error message was thrown:

ERROR: ERROR in SPR round (LIBPLL-2240): BL opt converged to a worse likelihood score by -546.001568175968714 units


This looks like the error is indeed related to RAxML rather than to the scheduler, which I thought of as one of the possible causes.

Any insight about what is the underlying cause of that error?


thanks in advance


Alexey Kozlov

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Sep 28, 2021, 4:56:54 PMSep 28
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Hello Nicolás,

could you please send me your input files and raxml-ng logs?

Thanks,
Alexey
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Nicolás Peñafiel

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Sep 28, 2021, 7:51:11 PMSep 28
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Hi Alexey, thanks for looking into it.
Here is the code I used:

#!/bin/bash

#SBATCH --job-name=boots_TVM_3

#SBATCH --time=0-3:00:00

#SBATCH --cpus-per-task=8

#SBATCH --mem=1G

module load StdEnv/2020  gcc/9.3.0  openmpi/4.0.3  raxml-ng/1.0.1

export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"

raxml-ng --bootstrap --msa TVM.raxml.rba --model TVM+I+G4  --seed 11 --threads ${OMP_NUM_THREADS} --prefix TVM_BS_3 --bs-trees 5000


Here are the documents:
- The MSA alignment
-The log file from RAxML-NG
- The log file from the scheduler

cheers

Nicolas
TVM.raxml.rba
TVM_BS_3.raxml.log
slurm-14666955.out

Alexey Kozlov

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Sep 30, 2021, 10:06:38 AMSep 30
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Hi Nicolas,

thanks for sending the files!

I can confirm there is a problem, and it looks very similar to the one which has been already
reported, which I am however still investigating and do not have a final fix yet.

In the meantime, you can use a simple workaround, just add

--blopt nr_safe

option to the command line.

As a side note, I would recommend reducing the number of bootstrap replicates, you can use e.g.

--bs-tree autoMRE{5000}

to perform automatic bootstrap convergence test.

Best,
Alexey

On 29.09.21 01:51, Nicolás Peñafiel wrote:
> Hi Alexey, thanks for looking into it.
> Here is the code I used:
>
> #!/bin/bash
>
> #SBATCH --job-name=boots_TVM_3
>
> #SBATCH --time=0-3:00:00
>
> #SBATCH --cpus-per-task=8
>
> #SBATCH --mem=1G
>
> module load StdEnv/2020  gcc/9.3.0  openmpi/4.0.3  raxml-ng/1.0.1
>
> export OMP_NUM_THREADS=*"${SLURM_CPUS_PER_TASK:-1}"*
>
> raxml-ng*--bootstrap --msa* TVM.raxml.rba*--model* TVM+I+G4 *--seed* 11*--threads*
> *${OMP_NUM_THREADS}**--prefix* TVM_BS_3*--bs-trees* 5000
> <https://groups.google.com/d/msgid/raxml/76eb9e65-16e2-4ad4-9baa-20661221a9c2n%40googlegroups.com?utm_medium=email&utm_source=footer
> <https://groups.google.com/d/msgid/raxml/76eb9e65-16e2-4ad4-9baa-20661221a9c2n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
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