Dandelion singularity (v0.2.4) cannot quantify mutation about dandelion HOT 6 CLOSED

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?

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@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

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Yup it’s just warnings and don’t need to worry about it.

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@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

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yes that's correct. as long as it doesn't error i.e. it says pre-processing finished, the warnings can be ignored.

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Noted and thank you so much :)

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