Error in "Refining phylogeny"

[biobakery]

Error in "Refining phylogeny"

[fasnicar]

Dear Jie,
Thanks for reporting this. I believe the problem is in the configuration file as I see in the error message that the placeholder #threads# has not been replaced with the parameters and the number of threads to use (16, in your case).
Can I ask you to report the section [tree2] of the config file and the command line that generated that config file?

Apart from this, the non-refined tree you already have should be good enough to continue your analysis. Tree refinement step might not always be needed.

Many thanks,
Francesco

[catcatzilla]

Hi Francesco,

The config file was generated using the phylophlan_write_default_configs.sh.
I saw the #threads# was not replaced. How should I replace this? Should it directly take the thread# from the command line?

[tree2]
program_name = /tigress/MOLBIO/local/bin/raxmlHPC-PTHREADS-SSE3
params = -p 1989 -m PROTCATLG
database = -t
input = -s
output_path = -w
output = -n
version = -v
command_line = #program_name# #params# #threads# #database# #output_path# #input# #output#

[fasnicar]

Hi

Thanks for your reply.
This is strange because if I run (which is what is present in the phylophlan_write_default_configs.sh script):

phylophlan_write_config_file -o supermatrix_aa.cfg \
    -d a \
    --db_aa diamond \
    --map_dna diamond \
    --map_aa diamond \
    --msa mafft \
    --trim trimal \
    --tree1 fasttree \
    --tree2 raxml \
    --overwrite \
    --verbose

the tree2 section looks like this:

[tree2]
program_name = /home/francesco/anaconda3/envs/ppa_test/bin/raxmlHPC-PTHREADS-SSE3
params = -p 1989 -m PROTCATLG
database = -t
input = -s
output_path = -w
output = -n
version = -v
command_line = #program_name# #params# #threads# #database# #output_path# #input# #output#
threads = -T

and correctly contains the definition for the #threads# placeholder (the order in which the definitions appear doesn't matter).

You can either try re-running the phylophlan_write_default_configs.sh script (or just the phylophlan_write_config_file command above) or you can simply manually add:

threads = -T

to the tree2 section of your config file.

[catcatzilla]

Hi Francesco,

Thank you! I just re-running phylophlan_write_default_configs.sh. The threads = -T showed up. Thanks so much!

[catcatzilla]

Hi Francesco,

Even with the threads information (16 here), it still give an error message.

[e] Command '['/tigress/MOLBIO/local/bin/raxmlHPC-PTHREADS-SSE3', '-p', '1989', '-m', 'PROTCATLG', '-T', '16', '-t', 'test/test_supermatrix_aa_output2/input_genomes_resolved.tre', '-w', '/projects/DONIA/jliu/Temporal/Phylophlan3/test/test_supermatrix_aa_output2', '-s', 'test/test_supermatrix_aa_output2/input_genomes_concatenated.aln', '-n', 'input_genomes_refined.tre']' returned non-zero exit status 127.

[e] error while executing
command_line: /tigress/MOLBIO/local/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 16 -t test/test_supermatrix_aa_output2/input_genomes_resolved.tre -w /projects/DONIA/jliu/Temporal/Phylophlan3/test/test_supermatrix_aa_output2 -s test/test_supermatrix_aa_output2/input_genomes_concatenated.aln -n input_genomes_refined.tre
stdin: None
stdout: None
env: {'SLURM_NODELIST': 'tiger-h21d1', 'SLURM_JOB_NAME': 'testPhylophlan_supermatrix_aa.sh', 'MANPATH': '/usr/share/man:/usr/local/share/man:/opt/puppetlabs/puppet/share/man', 'XDG_SESSION_ID': '55878', 'SLURMD_NODENAME': 'tiger-h21d1', 'SLURM_TOPOLOGY_ADDR': 'tiger-h21d1', 'HOSTNAME': 'tiger-h21d1', 'SELINUX_ROLE_REQUESTED': '', 'SLURM_NODE_ALIASES':

Best,
Jie

[fasnicar]

Hi Jie,

Check whether you have files from the previous RAxML execution in the output directory. RAxML won't run if it finds files from a previous execution.
If that's not the case, you can run the RAxML command from the error message:
/tigress/MOLBIO/local/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 16 -t test/test_supermatrix_aa_output2/input_genomes_resolved.tre -w /projects/DONIA/jliu/Temporal/Phylophlan3/test/test_supermatrix_aa_output2 -s test/test_supermatrix_aa_output2/input_genomes_concatenated.aln -n input_genomes_refined.tre

To better understand what RAxML doesn't like.

Thanks,
Francesco

[mcahn]

Hi Francesco,

An explanation of the missing "threads = -T": That happened because phylophlan_write_default_configs.sh output something that wasn't right for our environment. The script seemed to think astral was here:
astral-4.11.1/astral.4.11.1.jar
whereas in our environment it's a newer version, and the full path needs to be specified. So I edited the config files by hand and saved them. After my most recent update of phylophlan, I put my copy of the config files back, but my copy didn't contain the "threads = -T" line.

So a new installation would be correct as far as the threads line goes, though I'm not sure why the astral path/version is wrong.

Best,
Matthew

[fasnicar]

Many thanks Matthew for the explanation!

The ASTRAL path is hardcoded into the phylophlan_write_config_file.py because there is no automatic way to find if ASTRAL is installed in a system or not as, as far as I understood, there is practically no installation for ASTRAL it just needs java -jar astral.jar.
It is briefly described here: https://github.com/biobakery/phylophlan/wiki#supertree-or-gene-trees