Comments (8)
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
from phylophlan.
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#
from phylophlan.
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.
from phylophlan.
Hi Francesco,
Thank you! I just re-running phylophlan_write_default_configs.sh. The threads = -T showed up. Thanks so much!
from phylophlan.
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
from phylophlan.
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
from phylophlan.
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
from phylophlan.
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
from phylophlan.
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