Comments (6)
This is a lack of detailed documentation/bug, sorry - it should work if you run:
cp SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre.rooted SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre
run_gubbins.py --first-tree-builder rapidnj --first-model JC -p gubbins -c 32 -v SX519_Chromosomal_Ref_clean.core.full.aln --resume SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre
The problem is that Gubbins expects [tree file].phylip
to exist, which is not the case if (a) .rooted
is at the end, or (b) the file is in the temporary directory still. Apologies, I will try to fix this, or at least put in a more informative error message.
from gubbins.
Thank you for the quick response!
I reran as you suggested, but it unfortunately did the same thing and stopped in the same spot. Below are the details. Please let me know you need any other information.
If it helps, the [tree file].phylip from iteration 4 was not even in the temporary directory near as I can tell, although as you said it would not exist if it was rooted. When the slurm run requeue and reran in the middle of the night before I could stop it, it replaced anything that was not in the temporary directory near as I can tell, so if any of those files were necessary to restart, I would not have them.
Thanks for your time and help.
Code ran via slurm/sbatch per your advice after cping [tree file].tre.rooted to just {tree file}.tre file:
run_gubbins.py --first-tree-builder rapidnj --first-model JC -p gubbins -c 32 -v SX519_Chromosomal_Ref_clean.core.full.aln --resume SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre
Attached is the stdout file
post_github_advice_stdout.txt
ls -lah - Anything made on May 2nd was from the latest runs post your advice:
from gubbins.
My other run completed, and I was able to get all the expected outputs. So, I no longer need to restart from a killed and restarted slurm run with deleted non-temporary folder intermediates. If you no longer need this thread to be reminded of the documentation/bug you referenced, please feel free to close it. Thank you very much for your time, expertise, and wonderful tool!
from gubbins.
Thanks, I'm glad that run worked! Sorry for the lack of response - I will keep this open to remind me this needs fixing.
from gubbins.
No worries, can imagine you being very busy. Aye aye to keeping it open.
from gubbins.
I'm having the same problem resuming my run even if I have the .tre and .phylip files in my main folder.
from gubbins.
Related Issues (20)
- New ska version and masking HOT 5
- Gubbins input file error HOT 1
- File names with spaces cause error HOT 2
- Conda Gubbins 3.3.3 : Not able to install HOT 3
- RuntimeError: cannot cache function 'seq_to_int' HOT 5
- Conda Gubbins 3.3.4 : Not able to install HOT 11
- Unable to install gubbin HOT 6
- Multithreading not working on v3.3 HOT 1
- Can Gubbins be used on eukaryotic genomes? HOT 1
- Pyjar causing core dump HOT 7
- Latest Gubbins installs Gubbins 2.3.4 HOT 1
- Uninstalling gubbins 3.3.5 HOT 1
- Does Gubbins can be used for Mycobacterium tuberculosis? HOT 5
- Buffer overflow during model fitting HOT 6
- raxmlHPC-AVX2 error HOT 4
- REF and Reference do not match, is this expected? HOT 2
- Making a core SNP tree to go along with final.tre HOT 3
- How to restart a gubbins run using the --resume flag HOT 1
- Input File Error with Singularity/Apptainer
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gubbins.