Dandelion singularity (v0.2.4) cannot quantify mutation
Closed this issue · 6 comments
Description of the bug
Dear zktuong,
I have used this singularity for processing step which they were sucessful in many times ago.
Now, I am facing with this problem that the singularity cannot quantify mutation as attached figure.
If you have any suggestions, please let me know
Best regards,
Benjamaporn
Minimal reproducible example
No response
The error message produced by the code above
No response
OS information
No response
Version information
dandelion==0.2.4 pandas==1.4.3 numpy==1.22.4 matplotlib==3.5.2 networkx==2.8.4 scipy==1.8.1
Additional context
No response
hi @sbenjamaporn, not sure what's happened there but it looks like your singularity image decided to pull in your R from your local environment (outside the container).
maybe can you try to update your image and try again?
@zktuong Thanks for your suggestion,
Yes, I worked on R and found that it might relate with my local enviroment as you mentioned.
I changed the location of the singularity in another private server, and it can be sucessefully pre-processed !.
However, I got the warning messages from R as attached images.
Do you think it possibly affect my results or it is just the warmings ? (as I asked this question in the earlier discussion: #156 (comment))
![E2D888DD-6493-4B7B-B6E4-82EBBA12652B]
(https://github.com/zktuong/dandelion/assets/92794713/a4aa75c0-9173-4345-ab25-bf6ccbde496a)
Best regards,
Benjamaporn
Yup it’s just warnings and don’t need to worry about it.
@zktuong I got it!
Becase I did not use the command "singularity run -B $PWD" in the pre-processing step (I go to the sample folder, paste, and then run "sc-dandelion_latest.sif dandelion-preprocess --meta meta.csv" , so it used R from my local enviroment. However, I don't think it will impact my result since it show "Pre-processing finished". Do I understand this step correctly ?
For the next analysis, I will use "singularity run -B $PWD" to stop the warmings
Benjamaporn
yes that's correct. as long as it doesn't error i.e. it says pre-processing finished, the warnings can be ignored.
Noted and thank you so much :)