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KirstLab / asc_seurat

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Error: non-finite entries the input matrix. #17

Closed ib-nosuke closed 2 years ago

ib-nosuke commented 2 years ago

Hello. I am RUNing a Docker container of Asc Seurat. When I try to run the sample data, I get an error. I have not changed any values in the GUI. The place where the error occurs is in the clustering analysis. I get the message "Error: non-finite entries the input matrix." Then I noticed that the standard deviation value of the Elbow plot in PCA was wrong. From the bottom, the values are -1.132312e+240, 5.095405e+240, 1.132312e+241... I then tried to RUN the container on another server, but the error may or may not occur. It seems that the error always occurs on a specific host. Is there any way to determine the cause of this error?

fmalmeida commented 2 years ago

Hi @ib-nosuke,

Thank you for using Asc-Seurat and reporting this issue, which, indeed, is very strange. @ib-nosuke, if it happens again could you send us a screenshot of the error and of the part which you described the wrong values?

And about the issue, @wendelljpereira , do you have any thoughts? Maybe could be something related to the function single_cell_data_reso_umap which runs the clustering step? If so, we could add something to search for Inf values and replace them?

The problem here would be to locate the source of the issue 🤔

wendelljpereira commented 2 years ago

Hi @ib-nosuke,

I haven't seen this issue yet, so I am not sure what could be happening.

Are you analyzing your sample or the PBMC example dataset installed with the app?

If you only tried with your sample, is it in the 10x format as output by cell ranger? Could you analyze the PBMC dataset on the same computer and see if the problem persists?

Also, you are using the latest version of the app, v2.1, correct? It should be the latest if you copied the execution command from here: https://asc-seurat.readthedocs.io/en/latest/installation.html.

Last, what operating system do you have in that machine? I had multiple users reporting troubles installing Docker on certain versions of Windows (as Windows home). Since you can run the app, I assume the installation worked. But, I wonder if there is any incompatibility that could explain this issue.

Cheers, Wendell

ib-nosuke commented 2 years ago

@fmalmeida @wendelljpereira

Thank you for your reply. There are a number of procedures to follow to get a screenshot. I will reply to you as soon as it is ready.

I don't know if this is a hint, but... I just tried the command "docker logs Asc_Seurat"

xx:xx:xx Writing NN index file to temp file [path]. xx:xx:xx Searching Annoy index using 1 thread. search_k = 3000 xx:xx:xx Annoy recall = 2.299%. xx:xx:xx Commencing smooth kNN distance calibration using 1 thread xx:xx:xx 1305 smooth knn distance failures

The log was described as above. If the analysis is successful, it seems to be "Annoy recall = 100%". The data used for the analysis is ". /data/example_PBMC". The version of the image used is the latest. It failed on CentOS7 and Ubuntu20.04 on WSL2.

Thank you.

wendelljpereira commented 2 years ago

Hi @ib-nosuke,

I was not able to reproduce this issue in my system. We have released a new version of the app since then that you could test if you still have an interest. Alternatively, you could also download the app's source code, install the required packages, and run it using RStudio.

I am closing this issue if you have no further questions.

Best Regards, Wendell