Entering edit mode
4 months ago
nitinra ▴ 50
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!
Hi! How did you install
I used the conda environment to install it.
This is what I did:
This is what I get when I hit ete3 build check:
Well, the error is clear, right? Follow the instructions, install the dependencies using
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.
what error do you get when running:
iraun , can you please suggest how I can fix this?
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.
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:
You are almost there. The image is build in a way that you have to call the program name explicitly:
To simplify things, I would recommend putting an alias into your
If you are annoyed by the need for admin privileges (and happen to run GNU/Linux) you can also switch to Singularity instead.