"Muscle: MISSING" - with both conda and pip installs

[K2]

Hello! Thank you for ete3! I've had it running before but am trying to set up on a new machine and am running into the following: 

"Muscle: MISSING" error on build check whether I install with conda (as per http://etetoolkit.org/download/ with ete3_external_apps) or pip (following the https://github.com/etetoolkit/course example). I've tried adding muscle into the environments again (conda install -c etetoolkit muscle) and also "sudo apt install muscle", I can run muscle independent of ete3 but somehow ete3 can't see it and it throws errors in workflows that need muscle. I'm running Ubuntu 20.04 on WSL2. 

Thank you to anyone with any pointers!

[dengzi...@gmail.com]

Hi,

can you find ete3_apps/ folder in your bin/ folder? ete3_apps/ should at the same diretory with the ete3 program. you can find the path by run `which ete3`. 

as we never try managing ete3 in ubuntu 20, your question would be valueable

thanks 

[K2]

Hello! Yes, I see ete3_apps and muscle is there:

home/k6logc/miniconda3/envs/etecourse/bin/ete3_apps/bin/muscle

Thank you!

[ziqi deng]

ok, please try running your sample using muscle as the aligner to check if it works in the workflow. If it does, at least it doesn't affect its performance at the aspect of functionality.

 

K2 <k6l...@gmail.com> 于2020年12月30日周三 上午4:15写道：

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[K2]

Hello, It errors out unfinished, see below for command and output error message. Thank you!

$ xvfb-run ete3 build -a seqs2run.fasta -o checkMuscle/ --clearall -w muscle_default-none-none-fasttree_default

Toolchain path: /home/k6logc/miniconda3/envs/etecourse/bin/ete3_apps/bin

Toolchain version: unknown

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-k6logc'

['muscle_default-none-none-fasttree_default']

      --------------------------------------------------------------------------------

                  ETE build (3.1.2) - reproducible phylogenetic workflows

      Citation:

       Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and

       visualization of phylogenomic data. Mol Biol Evol (2016)

       doi:10.1093/molbev/msw046

      (Note that a list of the external programs used to complete all necessary

      computations will be shown after workflow execution. Those programs should

      also be cited.)

      --------------------------------------------------------------------------------

INFO -  Testing x86-64  portable applications...

       clustalo: OK - 1.2.4

      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]

         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: 1 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

INFO -  Starting ETE-build execution at Tue Dec 29 15:58:32 2020

INFO -  Output directory /mnt/c/users/k6logc/downloads/tempdeletable/checkMuscle

INFO -  Erasing all existing npr data...

INFO -  Reading aa sequences from seqs2run.fasta...

WRNG -  64 target sequences

INFO -  ETE build starts now!

INFO -   Updating tasks status: (Tue Dec 29 15:58:32 2020)

INFO -  Thread muscle_default-none-none-fasttree_default: pending tasks: 1 of sizes: 64

INFO -  Launched 0 jobs. 0(R), 0(W). Cores usage: 0/1

INFO -   (W) MultiSeqTask (64 aa seqs, MSF, /muscle_def...ee_default)

INFO -   (D) MultiSeqTask (64 aa seqs, MSF, /muscle_def...ee_default)

INFO -  Waiting 2 seconds

INFO -   Updating tasks status: (Tue Dec 29 15:58:35 2020)

INFO -  Thread muscle_default-none-none-fasttree_default: pending tasks: 1 of sizes: 64

INFO -   (W) AlgTask (64 aa seqs, Muscle, /muscle_def...ee_default)

INFO -  Waiting 2 seconds

INFO -  Launched 1 jobs. 1(R), 0(W). Cores usage: 1/1

INFO -   Updating tasks status: (Tue Dec 29 15:58:37 2020)

INFO -  Thread muscle_default-none-none-fasttree_default: pending tasks: 1 of sizes: 64

INFO -   (W) AlgTask (64 aa seqs, Muscle, /muscle_def...ee_default)

ERR  -        Job error reported: Job (muscle, 1d79ef)

ERR  -        Errors found in AlgTask (64 aa seqs, Muscle, /muscle_def...ee_default)

Traceback (most recent call last):

  File "/home/k6logc/miniconda3/envs/etecourse/lib/python3.6/site-packages/ete3/tools/ete_build_lib/scheduler.py", line 257, in schedule

    task.status = task.get_status(qstat_jobs)

  File "/home/k6logc/miniconda3/envs/etecourse/lib/python3.6/site-packages/ete3/tools/ete_build_lib/master_task.py", line 198, in get_status

    self.job_status = self.get_jobs_status(sge_jobs)

  File "/home/k6logc/miniconda3/envs/etecourse/lib/python3.6/site-packages/ete3/tools/ete_build_lib/master_task.py", line 306, in get_jobs_status

    raise TaskError(j, "Job execution error %s" %errorpath)

ete3.tools.ete_build_lib.errors.TaskError: Job execution error /mnt/c/users/k6logc/downloads/tempdeletable/checkMuscle/tasks/1d79ef27c525d0e3798176c4ebbb8cec

INFO -  Waiting 2 seconds

INFO -  Launched 0 jobs. 0(R), 0(W). Cores usage: 0/1

ERR  -  Thread muscle_default-none-none-fasttree_default contains errors:

ERR  -   ** AlgTask (64 aa seqs, Muscle, /muscle_def...ee_default)

ERR  -        -> Job (muscle, 1d79ef)

ERR  -        -> /mnt/c/users/k6logc/downloads/tempdeletable/checkMuscle/tasks/1d79ef27c525d0e3798176c4ebbb8cec

ERR  -          -> Job execution error /mnt/c/users/k6logc/downloads/tempdeletable/checkMuscle/tasks/1d79ef27c525d0e3798176c4ebbb8cec

ERR  -  Done with ERRORS

Data Error: Errors found in some tasks

[ziqi deng]

Thanks for the info, it looks weird indeed. 

 if you have intall muscle with "sudo apt install muscle" then I suggest you create a link to ete3_apps/bin/

try to run the following command:

$: ln -s $(which muscle) home/k6logc/miniconda3/envs/etecourse/bin/ete3_apps/bin/