
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 25-Dec-2020 10:13:49 as follows:

/opt/conda/conda-bld/pargenes_1608889558035/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/pargenes_src/../pargenes_binaries/raxml-ng --parse --log DEBUG --msa /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/fasta_files/msa4.fasta --model GTR+G --prefix /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/parse_run/results/msa4_fasta/msa4_fasta --threads 1

Analysis options:
  run mode: Alignment parsing and compression
  start tree(s): 
  random seed: 1608891229
  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: NONE/sequential

|noname|   |GTR+FO+G4m|   ||
[00:00:00] Reading alignment from file: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/fasta_files/msa4.fasta
Failed to load as IPHYLIP: Unable to parse PHYLIP file: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/fasta_files/msa4.fasta
 (LIBPLL-106): Invalid number of sequences in header
Failed to load as PHYLIP: Unable to parse PHYLIP file: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/fasta_files/msa4.fasta
 (LIBPLL-106): Invalid number of sequences in header
[00:00:00] Loaded alignment with 4 taxa and 50 sites
[00:00:00] Extracting partitions... 
[00:00:00] Checking the alignment...

WARNING: Fully undetermined columns found: 3

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/parse_run/results/msa4_fasta/msa4_fasta.raxml.reduced.phy
[00:00:00] Compressing alignment patterns... 

Alignment comprises 1 partitions and 38 patterns

Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 47 / 38
Gaps: 31.38 %
Invariant sites: 44.68 %


NOTE: Binary MSA file created: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/parse_run/results/msa4_fasta/msa4_fasta.raxml.rba

* Per-taxon CLV size (elements)                : 608
* Estimated memory requirements                : 1 MB

* Recommended number of threads / MPI processes: 1
* Maximum     number of threads / MPI processes: 1
* Minimum     number of threads / MPI processes: 1

Please note that numbers given above are rough estimates only. 
Actual memory consumption and parallel performance on your system may differ!

Alignment can be successfully read by RAxML-NG.


Execution log saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/parse_run/results/msa4_fasta/msa4_fasta.raxml.log

Analysis started: 25-Dec-2020 10:13:49 / finished: 25-Dec-2020 10:13:49

Elapsed time: 0.007 seconds

