Aborted (core dumped)

[Niohuruzh]

Hi raxml-ng team, I met A problem same with other user but still not solve. So I post my command and files as follow:

raxml-ng --all --msa all_aln_cut.fa --data-type AA --threads 10 --model VT+F+R8 --bs-trees 1000

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 28-Jan-2022 10:26:49 as follows:

raxml-ng --all --msa all_aln_cut.fa --data-type AA --threads 10 --model VT+F+R8 --bs-trees 1000

Analysis options:
  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
  start tree(s): random (10) + parsimony (10)
  bootstrap replicates: 1000
  random seed: 1643336809
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: PTHREADS (10 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: all_aln_cut.fa
[00:00:00] Loaded alignment with 123 taxa and 551 sites

WARNING: Sequences KAG0657364.1_Lanosterol_14-alpha-demethylase_Rhodotorula_mucilaginosa and S1_Rhodotorula_FUN_006333-T1_FUN_006333 are exactly identical!
WARNING: Duplicate sequences found: 1

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /media/leigod/f83cb121-4d63-4d87-8adf-a7bdefb24a63/home/leigod/data/huangjingjing/2sequenceresults/00.Rawdata/erg11/all_aln_cut.fa.raxml.reduced.phy

Alignment comprises 1 partitions and 551 patterns

Partition 0: noname
Model: VT+FC+R8
Alignment sites / patterns: 551 / 551
Gaps: 2.18 %
Invariant sites: 0.18 %


NOTE: Binary MSA file already exists: all_aln_cut.fa.raxml.rba


WARNING: You might be using too many threads (10) for your alignment with 551 unique patterns.
NOTE:    For the optimal throughput, please consider using fewer threads 
NOTE:    and parallelize across starting trees/bootstrap replicates.
NOTE:    As a general rule-of-thumb, please assign at least 200-1000 alignment patterns per thread.

[00:00:00] Generating 10 random starting tree(s) with 123 taxa
[00:00:00] Generating 10 parsimony starting tree(s) with 123 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 56 / 8960

Starting ML tree search with 20 distinct starting trees

[00:14:20] ML tree search #1, logLikelihood: -83352.170725
[00:26:30] ML tree search #2, logLikelihood: -83356.636227
[00:34:49] ML tree search #3, logLikelihood: -83547.705597
[00:43:31] ML tree search #4, logLikelihood: -83363.992846
[00:51:43] ML tree search #5, logLikelihood: -83393.795534
raxml-ng: /opt/conda/conda-bld/raxml-ng_1569616353378/work/libs/pll-modules/src/optimize/pll_optimize.c:1548: recomp_iterative_multi: Assertion `xguess[p] >= xmin && xguess[p] <= xmax' failed.
raxml-ng: /opt/conda/conda-bld/raxml-ng_1569616353378/work/libs/pll-modules/src/optimize/pll_optimize.c:1548: recomp_iterative_multi: As
sertion `xguess[p] >= xmin && xguess[p] <= xmax' failed.
Aborted (core dumped)

So what happened with my data? Looking for your reply There is my fasta file after alignment all_aln_cut.txt .

[amkozlov]

could please try to reproduce this with the latest raxml-ng v1.1 ?

chances are, this bug has been fixed already.

[Niohuruzh]

Thanks for your help. I'll install this version.

------------------ 原始邮件 ------------------ 发件人: "amkozlov/raxml-ng" @.>; 发送时间: 2022年1月28日(星期五) 晚上7:12 @.>; @.@.>; 主题: Re: [amkozlov/raxml-ng] Aborted (core dumped) (Issue #135)

could please try to reproduce this with the latest raxml-ng v1.1 ?

chances are, this bug has been fixed already.

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.Message ID: @.***>

[amkozlov]

If the issue still exists, please reopen,