Ete3 build - ValueError: Error parsing Phyml result

Question

[nitinra]

Hello,

I am using ete3 build to build a phylogeny of my target species. I ran the following command:

ete3 build -a eteinput.faa --cogs outfile.tab -o test1_results -m sptree_fasttree_85 -w full_modeltest_bootstrap  --clearall --cpu 20

I am getting the following error:

Traceback (most recent call last):

  File "/home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin/pmodeltest.py", line 582, in <module> main()

  File "/home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin/pmodeltest.py", line 64, in main
    job_list = parse_jobs(job_list, opts.algt)

File "/home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin/pmodeltest.py", line 181, in parse_jobs
    numspe, lnl, dic = parse_stats(fname)

File "/home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin/pmodeltest.py", line 364, in parse_stats
    raise ValueError("Error parsing Phyml result %s" %path)

ValueError: Error parsing Phyml result /media/nitin/toshiba_hdd/Work/Phd/Chapter_4/data/test1_results/input/5402a3c764d1d210bed8c3000dd6673b.201_phyml_stats_JTT+I.txt

How do I fix this error?

Thank you so much!

[iraun]

Hi! How did you install ete3 ?

[nitinra]

I used the conda environment to install it.

[iraun]

Following this?

conda create -n ete3 python=3
conda activate ete3
conda install -c etetoolkit ete3 ete_toolchain
ete3 build check

[nitinra]

This is what I did:

conda create -n ete3 python=3
conda activate ete3
pip install --upgrade ete3
ete3 build check

[nitinra]

This is what I get when I hit ete3 build check:

(ete3) nitin@nitindebian:/media/nitin/toshiba_hdd/Work/Phd/Chapter_4/data$ ete3 build check
Current Toolchain path: /home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin 
Current Toolchain version: unknown
       clustalo: OK - 1.2.4
         codeml: OK - AAML in paml version 4.8a, July 2014
      dialigntx: OK - This is DIALIGN-TX Version 1.0.2 - A Multiple Sequence alignment program.
       fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (1 threads):
         iqtree: OK - IQ-TREE multicore version 1.5.5 for Linux 64-bit built Jun  2 2017
         kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
          mafft: OK - MAFFT v6.861b (2011/09/24)
         muscle: MISSING
          phyml: OK - . This is PhyML version 20160115.
     pmodeltest: OK - pmodeltest.py v1.4
          raxml: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
 raxml-pthreads: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
         readal: OK - readAl v1.4.rev6 build[2012-02-02]
            slr: MISSING
         statal: OK - statAl v1.4.rev6 build[2012-02-02]
        tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
         trimal: OK - trimAl v1.4.rev6 build[2012-02-02]

WARNING: 2 external tools seem to be missing or unfunctional
Install using conda (recomended):
 conda install -c etetoolkit ete3_external_apps
or manually compile by running:
 ete3 upgrade-external-tools

[iraun]

Well, the error is clear, right? Follow the instructions, install the dependencies using conda, not pip.

[nitinra]

The dependencies do not install when I use conda and the workaround answer that I found most commonly used was to install it using pip. The authors on GitHub also mentioned the same thing.

[iraun]

what error do you get when running:

conda install -c etetoolkit ete3 ete_toolchain ete3_external_apps

[nitinra]

nitin@nitindebian:/media/nitin/toshiba_hdd/Work/Phd/Chapter_4/data$ conda activate ete3_new
(ete3_new) nitin@nitindebian:/media/nitin/toshiba_hdd/Work/Phd/Chapter_4/data$ conda install -c etetoolkit ete3 ete_toolchain ete3_external_apps
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - ete3_external_apps -> python[version='2.7.*|3.4.*']

Your python: python=3

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package openblas conflicts for:
ete_toolchain -> slr=1.4.3 -> openblas
ete3_external_apps -> openblas

Package openssl conflicts for:
ete3 -> python -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.0.2l,<1.0.3a|1.1.*']
python=3 -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.0.2l,<1.0.3a']
ete3_external_apps -> python=2.7 -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.0.2l,<1.0.3a']

Package libuuid conflicts for:
python=3 -> libuuid[version='>=1.0.3,<2.0a0']
ete3 -> python -> libuuid[version='>=1.0.3,<2.0a0']

Package libopenblas conflicts for:
ete3 -> numpy -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.20,<1.0a0|>=0.3.3,<1.0a0|>=0.3.21,<1.0a0']
ete3_external_apps -> openblas -> libopenblas[version='0.3.10|0.3.13|0.3.17|0.3.18|0.3.20|0.3.20|0.3.21|0.3.6|0.3.6|0.3.6|0.3.3|0.3.3|0.3.3|>=0.3.2,<0.3.3.0a0|>=0.2.20,<0.2.21.0a0',build='h5a2b251_2|hf726d26_0|h043d6bf_0|h043d6bf_1|h043d6bf_0|hf726d26_1|h4367d64_0|h5a2b251_0|h5a2b251_1|h5a2b251_0|h5a2b251_3|h5a2b251_2|h5a2b251_1']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - python=3 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

[nitinra]

iraun , can you please suggest how I can fix this?

[Matthias Zepper]

Exactly due to similar issues with conda, I have almost completely switched to running containerized applications. Usually one can find pre-build Docker container images of any application on Docker Hub, which can also be seamlessly converted to Singularity images for HPC environments.

I have never used that particular software, but there are multiple ete3 container images available. This Docker image looks pretty good to me and Galaxy even has an existing Singularity image.

[nitinra]

Thank you so much for your response. I have never used docker. Is there a tutorial page you'd recommend to learn to run docker? TIA!

I installed docker engine and used docker pull to download it. However, I am unable to run it using this command:

sudo docker run -it cbcrg/ete3 -h

docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "-h": executable file not found in $PATH: unknown.
ERRO[0001] error waiting for container: context canceled

[Matthias Zepper]

You are almost there. The image is build in a way that you have to call the program name explicitly:

sudo docker run -it cbcrg/ete3 ete3 version

To simplify things, I would recommend putting an alias into your ~/.bashrc or ~/.zprofile:

alias ete3="docker run -itv `pwd`:`pwd` -w `pwd` -u $(id -u):$(id -g) cbcrg/ete3 ete3"

If you are annoyed by the need for admin privileges (and happen to run GNU/Linux) you can also switch to Singularity instead.