Hanging at Parsing MSA

[kevinmyers]

We are attempting to make a tree using RAxML-ng adaptive (v1.2.1-adaptive). The alignment file (attached in .txt form for GitHub) was created using jackhmmer in Stockholm format and then converted to aligned fasta format:

jackhmmer -A mDHFR.sto -o mDHFR.out.txt mDHFR.fasta uniref90.fasta /hmmer-3.1b2-linux-intel-x86_64/binaries/esl-reformat -u -o C_tails_full_seqs.fasta afa mDHFR.sto

When we run raxml-ng-adaptive in the --parse option, it hangs at the Predicting difficulty of the MSA . . . step:

/opt/bifxapps/raxml-ng-adaptive/bin/raxml-ng-adaptive --parse --msa C_tails_full_seqs.fasta -model LG+G8+F --prefix T1

RAxML-NG v. 1.2.1-adaptive released on 11.04.2024 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz, 32 cores, 251 GB RAM

RAxML-NG was called at 15-Oct-2024 09:24:41 as follows:

/opt/bifxapps/raxml-ng-adaptive/bin/raxml-ng-adaptive --parse --msa C_tails_full_seqs.fasta -model LG+G8+F --prefix T1

Analysis options:
  run mode: Alignment parsing and compression
  start tree(s): 
  random seed: 1729002281
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  logLH epsilon: general: 0.100000, brlen-triplet: 1000.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (auto)

[00:00:00] Reading alignment from file: C_tails_full_seqs.fasta
[00:00:00] Loaded alignment with 1497 taxa and 2550 sites

Alignment comprises 1 partitions and 2403 patterns

Partition 0: noname
Model: LG+FC+G8m
Alignment sites / patterns: 2550 / 2403
Gaps: 87.51 %
Invariant sites: 26.47 %

[00:00:00] Adaptive mode: Predicting difficulty of the MSA ...

We have let it run over a weekend and it has shown no progress. We have successfully used raxml-ng-adaptive (and regular raxml-ng) in the past so I'm confused what would be causing this issue. Any help would be greatly appreciated.

C_tails_full_seqs.fasta.txt

[amkozlov]

Hi @kevinmyers, could you please upgrade to the latest version and try again?

With RAxML-NG v. 1.2.1-adaptive released on 02.10.2024 It took ~7min on my laptop.

[kevinmyers]

Will do, thanks! I'll let you know how it works after the IT staff installs the new version on our server cluster.

Just out of curiosity, I assume this must be a typo then and should be 2023?

RAxML-NG v. 1.2.1-adaptive released on 11.04.2024

[amkozlov]

now it's April 11th, 2024 :)

please pull the most recent version from github:

https://github.com/amkozlov/raxml-ng/wiki/Installation#building-adaptive-branch

[kevinmyers]

That's what I get for reading it in the US date format - apologies!

[kevinmyers]

We updated to the newest version (RAxML-NG v. 1.2.2-master released on 30.04.2024) and we were able to run the parse command (and the main command) no problem. Thanks for your help!