FastTree not found, installed and in PATH

[Jiffin Paulose]

Currently attempting to run Phylophlan2 on a cluster running CentOS 3.10 .  I receive the following:

[e] Command '['FastTree']' returned non-zero exit status 1.

[e] program not installed or not present in the system path

    command_line: FastTree

           stdin: None

          stdout: None

             env: None

I have confirmed that running the command "FastTree" (without quotes) works in the CLI, 

Thanks for your help!

[Jiffin Paulose]

Here is the output of the script:

PhyloPhlAn version 0.24 (25 October 2018)

Command line: phylophlan2.py -i klebsiella-aerogenes -d phylophlan -f proteinconfig.cfg -t a --diversity medium --nproc 12 --accurate --output_folder klebsiella-aerogenes --verbose

Automatically setting "input=klebsiella-aerogenes" and "input_folder=/home/jkpa222/phylophlan"

"medium-accurate" preset

Setting "sort=True" because "database=phylophlan"

Setting "min_num_markers=100" since no value has been specified and the "database=phylophlan"

Arguments: {'input': 'klebsiella-aerogenes', 'clean': None, 'database': 'phylophlan', 'db_type': 'a', 'config_file': 'proteinconfig.cfg', 'diversity': 'medium', 'meta': False, 'accurate': True, 'fast': False, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 12, 'min_num_proteins': 1, 'min_len_protein': 50, 'min_num_markers': 100, 'trim': 'gappy', 'not_variant_threshold': 0.99, 'subsample': <function fifty at 0x7f7b89c83c80>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x7f7b89c83f28>, 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.85, 'min_num_entries': 4, 'maas': None, 'remove_only_gaps_entries': False, 'mutation_rates': False, 'input_folder': '/home/jkpa222/phylophlan/klebsiella-aerogenes', 'data_folder': 'klebsiella-aerogenes/klebsiella-aerogenes_phylophlan/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': 'phylophlan_substitution_matrices/', 'submod_folder': 'phylophlan_substitution_models/', 'configs_folder': 'phylophlan_configs/', 'output_folder': 'klebsiella-aerogenes/klebsiella-aerogenes_phylophlan', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'verbose': True}

Loading configuration file "proteinconfig.cfg"

Checking configuration file

Checking "muscle -version"

Checking "usearch -version"

Checking "blastn -version"

Checking "FastTree"

[Francesco Asnicar]

Hi,

Many thanks for trying the new version of PhyloPhlAn.

This is strange, so I need some more info to understand what's happening. Can you provide:

  1) the PhyloPhlAn version you're using? You should have "0.24 (25 October 2018)" and if you rung hg head you should see that the commit is 7c38e19.

  2) the configuration file? Has it been generated with the "phylophlan_write_default_configs.sh" script or was it present in the repository?

  3) result of:

$ echo $PATH

$ which FastTree

$ whereis FastTree

Many thanks,

Francesco

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[Jiffin Paulose]

(ppa2) [jkpa222@login-0-1 phylophlan]$ python phylophlan2.py --version

PhyloPhlAn version 0.24 (25 October 2018)

Config file:

(ppa2) [jkpa222@login-0-1 phylophlan]$ cat proteinconfig.cfg

[msa]

command_line = #program_name# #params# #input# #output#

output = -out

program_name = muscle

params = -quiet -maxiters 2

version = -version

input = -in

[db_aa]

command_line = #program_name# #params# #input# #output#

output = -output

program_name = usearch

params = -quiet

version = -version

input = -makeudb

[map_dna]

command_line = #program_name# #params# #input# #database# #output#

database = -db

output = -out

program_name = blastn

params = -outfmt 6 -max_target_seqs 1000000

version = -version

input = -query

[gene_tree1]

params = -quiet -mlacc 2 -slownni -spr 4 -fastest -mlnni 4 -no2nd -lg

command_line = #program_name# #params# #output# #input#

output = -out

program_name = FastTree

[map_aa]

command_line = #program_name# #params# #threads# #input# #database# #output#

output = -blast6out

database = -db

threads = -threads

program_name = usearch

params = -quiet -evalue 1e-10 -maxaccepts 8 -maxrejects 32

version = -version

input = -ublast

[tree1]

params = -quiet -mlacc 2 -slownni -spr 4 -fastest -mlnni 4 -no2nd -lg

command_line = #program_name# #params# #output# #input#

environment = OMP_NUM_THREADS=3

output = -out

program_name = FastTree

echo $PATH

/home/jkpa222/miniconda3/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/usr/local/bin:/home/jkpa222/lastz/bin:/home/jkpa222/sibelia/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/usr/local/bin:/home/jkpa222/lastz/bin:/home/jkpa222/sibelia/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/usr/local/bin:/home/jkpa222/lastz/bin:/home/jkpa222/sibelia/bin:/home/jkpa222/miniconda3/envs/ppa2/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/miniconda3/bin:/home/jkpa222/usr/local/bin:/home/jkpa222/lastz/bin:/home/jkpa222/sibelia/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/ibutils/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/dell/srvadmin/bin:/home/jkpa222/edirect:/home/jkpa222/bin:/home/jkpa222/bio/phyml/src:/home/jkpa222/bio/ncbi/SRA/bin:/home/jkpa222/bio/Raxml/standard-RAxML:/home/jkpa222/bio/augustus/config:/home/jkpa222/bio/augustus/bin:/home/jkpa222/bio/cufflinks:/home/jkpa222/bio/augustus/scripts:/home/jkpa222/bio/snap:/home/jkpa222/bio/ncbi/blast/bin:/home/jkpa222/bio/maker/exe/exonerate:/home/jkpa222/bio/maker/exe/RepeatMasker:/home/jkpa222/bio/maker/bin:/home/jkpa222/DLs/SRAToolkit/Tools/bin:/home/jkpa222/bio/RepeatMasker/:/home/jkpa222/bio/rmblast/bin:/home/jkpa222/scratch/xscript/FastQC/:/home/jkpa222/edirect:/home/jkpa222/edirect:/home/jkpa222/tools:/home/jkpa222/edirect:/home/jkpa222/tools  

which FastTree

~/tools/FastTree

whereis FastTree

FastTree: /home/jkpa222/tools/FastTree

[Jiffin Paulose]

I should also note that when I try to run the write_default_configs.sh script (the one listed under committed 7c38e19, I get the error "-d: command not found".  The error persists even if I change "-d" to "--dbtype"

[Francesco Asnicar]

Strange, that has been solved with that commit, even though the phylophlan_write_default_config.sh script expects to find in the system path phylophlan_write_config_file.py script.

Can you run an:

$ hg pull && hg update

Just to make sure that, and if you like to send the:

$ head phylophlan_write_default_config.sh

I can confirm that those correspond to the latest available.

Thanks,

Francesco

On Thu, Nov 1, 2018 at 3:56 PM Jiffin Paulose <jpau...@gmail.com> wrote:

I should also note that when I try to run the write_default_configs.sh script (the one listed under committed 7c38e19, I get the error "-d: command not found".  The error persists even if I change "-d" to "--dbtype"

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[Jiffin Paulose]

(ppa2) [jkpa222@login-0-1 phylophlan]$ hg pull && hg update

pulling from https://bitbucket.org/nsegata/phylophlan

searching for changes

no changes found

0 files updated, 0 files merged, 0 files removed, 0 files unresolved

(ppa2) [jkpa222@login-0-1 phylophlan]$ head phylophlan_write_default_configs.sh

#!/bin/bash

 

 

 # supermatrix_nt.cfg

# ./phylophlan_write_config_file.py -o supermatrix_nt.cfg \

   phylophlan_write_config_file.py -o supermatrix_nt.cfg \

# ./phylophlan_write_config_file.py -o supermatrix_nt.cfg \

     --db_type n \

     --db_dna makeblastdb \

     --map_dna blastn \

[Jiffin Paulose]

Output of the commit update i mentioned

(ppa2) [jkpa222@login-0-1 phylophlan]$ head phylophlan_write_default-configs-commit.sh

 #!/bin/bash 

 # supermatrix_nt.cfg

# ./phylophlan_write_config_file.py -o supermatrix_nt.cfg \

 python phylophlan_write_config_file.py -o supermatrix_nt.cfg \

# ./phylophlan_write_config_file.py -o supermatrix_nt.cfg \

     -d n \

     --db_dna makeblastdb \

     --map_dna blastn \

     --msa mafft \

 

[Francesco Asnicar]

The commented line(s) below the phylophlan_write_config_file.py is causing the error.

Those have been removed with the 7c38e19 commit (https://bitbucket.org/nsegata/phylophlan/commits/7c38e1993483e8580da4b475bdd2faf2392868eb).

The first 10 lines, in fact, should look like:

#!/bin/bash

# supermatrix_nt.cfg

# ./phylophlan_write_config_file.py -o supermatrix_nt.cfg \

phylophlan_write_config_file.py -o supermatrix_nt.cfg \

    -d n \

    --db_dna makeblastdb \

    --map_dna blastn \

    --msa mafft \

I'm working on the FastTree issue, I hope to have some good news soon.

Thanks,

Francesco

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[Jiffin Paulose]

Thanks for the information.  I've been able to get the default configs written, but I've discovered that the script only fails when it's in the compute node.  In other words, if I run it straight off the command line, it works fine.  But, if I place the script into a bash executable and submit it into slurm queue, it fails when checking for FastTree (also fails when checking for raxmlHPC, which is also installed and in the PATH).  

I think this may be a problem with how the compute node is handling things, but I'm not sure why.

[Francesco Asnicar]

I see, indeed then it is the way the environment is handled by the node.

Alternatively, you can substitute the "FastTree" command with the full path to the executable, at this point this is not dependent on the environment.

Many thanks,

Francesco

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