after parse:
########################
#    PARGENES v1.2.0   #
########################

2020-12-25 10:13:32.436037
ParGenes was called as follow:
/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.py -a /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/fasta_files -o /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes -r /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/raxml_global_options.txt -c 4 -m -b 3 -s 3 -p 3 --use-astral --modeltest-global-parameters /opt/conda/conda-bld/pargenes_1608889558035/work/tests/smalldata/only_1_models.txt --scheduler fork

[0:00:00] end of MSAs initializations
Binaries directory: /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
Calling mpi-scheduler: /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/mpi-scheduler --fork-scheduler 4 /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 /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/parse_run/parse_command.txt /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/parse_run --threads-arg --threads
Logs will be redirected to /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/parse_run/logs.txt
  Number of families: 5
  Average number of taxa: 4
  Max number of taxa: 10
  Average number of sites: 33
  Max number of sites: 50
  Recommended MAXIMUM number of cores: 2
[Warning] [0:00:00] Found 1 invalid MSAs (see /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/invalid_msas.txt)
[0:00:00] end of parsing mpi-scheduler run
[0:00:00] end of anlysing parsing results
Calling mpi-scheduler: /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/mpi-scheduler --fork-scheduler 4 /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/modeltest-ng /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/modeltest_run/modeltest_command.txt /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/modeltest_run --threads-arg -p
Logs will be redirected to /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/modeltest_run/logs.txt
[0:00:00] end of modeltest mpi-scheduler run
[0:00:00] end of parsing  modeltest results
Calling mpi-scheduler: /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/mpi-scheduler --fork-scheduler 4 /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 /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/parse_run/parse_command.txt /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/parse_run --threads-arg --threads
Logs will be redirected to /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/parse_run/logs.txt
  Number of families: 5
  Average number of taxa: 4
  Max number of taxa: 10
  Average number of sites: 33
  Max number of sites: 50
  Recommended MAXIMUM number of cores: 2
[Warning] [0:00:00] Found 1 invalid MSAs (see /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/invalid_msas.txt)
[0:00:00] end of the second parsing step
Calling mpi-scheduler: /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/mpi-scheduler --fork-scheduler 4 /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 /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/mlsearch_run/mlsearch_command.txt /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/mlsearch_run --threads-arg --threads
Logs will be redirected to /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/mlsearch_run/logs.txt
[0:00:01] end of mlsearch mpi-scheduler run
[0:00:01] end of selecting the best ML tree
[0:00:01] end of bootstraps concatenation
Writing supports commands in /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/supports_run/supports_commands.txt
Calling mpi-scheduler: /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/mpi-scheduler --fork-scheduler 4 /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 /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/supports_run/supports_commands.txt /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/supports_run --threads-arg --threads
Logs will be redirected to /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/supports_run/logs.txt
[0:00:01] end of supports mpi-scheduler run
Astral additional parameters:
[]
ParGenes/Astral: 4 gene trees (with support values) were found in ParGenes output directory
Starting astral... Logs will be redirected to /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes/astral_run/astral_logs.txt
[0:00:01] END OF THE RUN OF pargenescore.pyc
