Running RAxML-ng with GTDBTk MSA file
Kevin Myers
Then I ran the Parse command to determine the memory requirements and thread recommendations:
raxml-ng --parse --msa gtdbtk.bac120.msa.forRAxML.fasta --model LG+G8+F --prefix T2
I then ran RAxML-ng on the RBA file created during Parse. Since I'm running on a machine with 300 GB RAM and 16 cores (Parse recommended 14 cores), I decided to increase the tree numbers:
raxml-ng --msa T2.raxml.rba --model LG+G8+F --prefix T3 --threads 14 --seed 2 --tree pars{25},rand{25}
The program has been running for over a week at this point. Here is the Log information:
RAxML-NG v. 0.9.0 released on 20.05.2019 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
RAxML-NG was called at 12-Jul-2021 10:34:23 as follows:
raxml-ng --msa T2.raxml.rba --model LG+G8+F --prefix T3 --threads 14 --seed 2 --tree pars{25},rand{25}
Analysis options:
run mode: ML tree search
start tree(s): random (25) + parsimony (25)
random seed: 2
tip-inner: OFF
pattern compression: ON
per-rate scalers: OFF
site repeats: ON
fast spr radius: AUTO
spr subtree cutoff: 1.000000
branch lengths: proportional (ML estimate, algorithm: NR-FAST)
SIMD kernels: AVX2
parallelization: PTHREADS (14 threads), thread pinning: OFF
WARNING: The model you specified on the command line (LG+G8+F) will be ignored
since the binary MSA file already contains a model definition.
If you want to change the model, please re-run RAxML-NG
with the original PHYLIP/FASTA alignment and --redo option.
[00:00:00] Loading binary alignment from file: T2.raxml.rba
[00:00:02] Alignment comprises 23478 taxa, 1 partitions and 5040 patterns
Partition 0: noname
Model: LG+FC+G8m
Alignment sites / patterns: 5040 / 5040
Gaps: 11.56 %
Invariant sites: 0.00 %
NOTE: Per-rate scalers were automatically enabled to prevent numerical issues on taxa-rich alignments.
NOTE: You can use --force switch to skip this check and fall back to per-site scalers.
[00:00:03] Generating 25 random starting tree(s) with 23478 taxa
[00:00:04] Generating 25 parsimony starting tree(s) with 23478 taxa
It looks like there are 23,748 taxa - including the 20 text taxa and all the GTDBTk reference taxa. The MSA is amino acid sequences for the 37 protein sequences GTDBTk uses for classification, concatenated for each sample in FASTA format.
I've never used RAxML before, so I'm not sure if this time frame is expected? Any advice would be appreciated.
Thanks!
Kevin
Alexey Kozlov
(sorry for late response, your mail ended up in my spam folder)
first of all, please upgrade to the latest raxml-ng 1.0.3, which contains many bugfixes/improvements
compared to v0.9.0:
https://github.com/amkozlov/raxml-ng/releases/tag/1.0.3
Second, you'd probably be better off with using raxml-ng to build a backbone tree from the reference
sequences, and then use EPA-NG to place the metagenomic samples:
https://github.com/Pbdas/epa-ng
Best,
Alexey
On 19.07.21 18:05, Kevin Myers wrote:
> I am trying to contract a tree with RAxML-ng using the results from GTDBTk analysis for my
> metagenomic samples. GTDBTk has generated a MSA file that I am using.
>
> I started with the following command to check the MSA for errors:
>
> Then I ran the Parse command to determine the memory requirements and thread recommendations:
>
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Kevin Myers
Alexey Kozlov
Alexey
On 20.08.21 16:23, Kevin Myers wrote:
> Thank you! This response also ended up in my spam folder, so apologies for my late reply.
>
> I was able to get the newest version of RAxML-ng running smoothly to build the backbone tree as you
> suggested!
>
> Thanks again for your help!
>
> Kevin
>
> On Friday, July 23, 2021 at 3:43:00 AM UTC-5 alexei...@gmail.com wrote:
>
> Hi Kevin,
>
> (sorry for late response, your mail ended up in my spam folder)
>
> first of all, please upgrade to the latest raxml-ng 1.0.3, which contains many
> bugfixes/improvements
> compared to v0.9.0:
>
> https://github.com/amkozlov/raxml-ng/releases/tag/1.0.3
> <https://github.com/amkozlov/raxml-ng/releases/tag/1.0.3>
>
> Second, you'd probably be better off with using raxml-ng to build a backbone tree from the
> reference
> sequences, and then use EPA-NG to place the metagenomic samples:
>
> Best,
> Alexey
>
> On 19.07.21 18:05, Kevin Myers wrote:
> > I am trying to contract a tree with RAxML-ng using the results from GTDBTk analysis for my
> > metagenomic samples. GTDBTk has generated a MSA file that I am using.
> >
> > I started with the following command to check the MSA for errors:
> >
> > *raxm*l-ng --check --msa gtdbtk.bac120.msa.edited2.fasta --model LG+G8+F --prefix T1
> >
> > Then I ran the Parse command to determine the memory requirements and thread recommendations:
> >
> > *raxm*l-ng --parse --msa gtdbtk.bac120.msa.forRAxML.fasta --model LG+G8+F --prefix T2
> >
> > I then ran RAxML-ng on the RBA file created during Parse. Since I'm running on a machine with
> 300 GB
> > RAM and 16 cores (Parse recommended 14 cores), I decided to increase the tree numbers:
> >
> > raxml-ng --msa T2.raxml.rba --model LG+G8+F --prefix T3 --threads 14 --seed 2 --tree
> pars{25},rand{25}
> >
> > The program has been running for over a week at this point. Here is the Log information:
> >
> > RAxML-NG v. 0.9.0 released on 20.05.2019 by The Exelixis Lab.
> >
> > Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
> >
> > Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
> >
> <https://groups.google.com/d/msgid/raxml/7bff2fb2-eb20-4c8f-bb92-a7f2066822ecn%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
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