[BUG] Cellxgene failing to launch h5ad files

[chryssiebrown]

Describe the bug
Receive the following error message when launching recently generated h5ad files

Error: File not found or is inaccessible. File must be an .h5ad object

I can launch other h5ad files in the same google drive folder and am also able to launch the files that I am having issues with when I use a different iMAC

To Reproduce
Steps to reproduce the behavior:
From the terminal:
cellxgene launch /Users/xxxx/Library/CloudStorage/GoogleDrive-xxxx/My\ Drive/xxx\ xx/cellxgene/xxxx.h5ad

Expected behavior
Files would usually launch

Screenshots
If applicable, add screenshots to help explain your problem.

Version (please complete the following information):

• MAC
• Safari
• MAC OS Ventura 13.4

Additional context
Add any other context about the problem here.

[MaximilianLombardo]

Hey Chryssie - thanks - can you launch an h5ad with cellxgene when they are saved outside of your google drive folder?

Max

[chryssiebrown]

Hi Max, I get the same error message if I try and launch it from e.g. my Downloads folder, Chryssie

…

On Aug 16, 2023, at 4:24 PM, MaximilianLombardo ***@***.***> wrote: Hey Chryssie - thanks - can you launch an h5ad with cellxgene when they are saved outside of your google drive folder? Max — Reply to this email directly, view it on GitHub <#2625 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOR6PHCPQ77O7HOTTP26PX3XVUT7PANCNFSM6AAAAAA3S3VWAE>. You are receiving this because you authored the thread.

[chryssiebrown]

Hi Max,Just following up on this - let me know if there is anything else I can try,Thanks,ChrysOn 16 Aug 2023, at 17:05, Chrysothemis Brown ***@***.***> wrote:Hi Max,I get the same error message if I try and launch it from e.g. my Downloads folder,ChryssieOn Aug 16, 2023, at 4:24 PM, MaximilianLombardo ***@***.***> wrote:Hey Chryssie - thanks - can you launch an h5ad with cellxgene when they are saved outside of your google drive folder?Max—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[Fougere87]

Hi everyone,
I had the same problem here when trying to read a recent h5ad file through a docker instance of cellxgene.
What is strange is that all my "old" h5ad files could be read without any problem.
No problem loading the file in scanpy as well

It seems to be related to old versions of python because numba cannot update with a python env below 3.8.
Using 3.9 or 3.10 python or env everything works perfectly.

Hope it helps !

[MaximilianLombardo]

@Fougere87 thanks for the suggestion! @chryssiebrown what version of python are you running? Does this fix the issue for you?

Hey @chryssiebrown, if that does not solve your problem, are you able to share the data file that is giving you trouble? Would you also be able to share the following info?

• With what version was the file created?
• Is that the same version as the files that work with CELLxGENE currently?
• Could you also share the more complete stack trace here?

Apologies for the inundation of questions

[chryssiebrown]

Thanks for the suggestion - the problem sounds identical, I could read old h5ad files without any problem but only have issues with recent h5ad. I checked the version of python though and it’s 3.9.6 which should be ok? I can try updating. I will check the version of python used for creating recent vs old files, Thanks, Chrys

…

On Aug 24, 2023, at 11:51 AM, MaximilianLombardo ***@***.***> wrote: @Fougere87 <https://github.com/Fougere87> thanks for the suggestion! @chryssiebrown <https://github.com/chryssiebrown> what version of python are you running? Does this fix the issue for you? Hey @chryssiebrown <https://github.com/chryssiebrown>, if that does not solve your problem, are you able to share the data file that is giving you trouble? Would you also be able to share the following info? With what version was the file created? Is that the same version as the files that work with CELLxGENE currently? Could you also share the more complete stack trace here? Apologies for the inundation of questions — Reply to this email directly, view it on GitHub <#2625 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOR6PHGV6VNC7CWP4BNVMTDXW52ANANCNFSM6AAAAAA3S3VWAE>. You are receiving this because you were mentioned.

[yyoshiaki]

Hi everyone,

I got the same error with the docker container in several independent environments. You could reproduce the error as follows;

1. Docker setup

git clone https://github.com/chanzuckerberg/cellxgene.git
cd cellxgene
docker build . -t cellxgene

2. h5ad prep

import scanpy as sc

adata = sc.datasets.pbmc3k_processed()
adata.write('pbmc3k.h5ad')

my env

python 3.9.16
scanpy==1.9.3 anndata==0.9.1 umap==0.5.3 numpy==1.22.4 scipy==1.9.1 pandas==1.3.5 scikit-learn==1.2.2 statsmodels==0.14.0 python-igraph==0.10.4 pynndescent==0.5.10

3. launch cellxgene

docker run -v "$PWD:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad 

Error

[cellxgene] Starting the CLI...
[cellxgene] Loading data from pbmc3k.h5ad.
Error: File not found or is inaccessible. File must be an .h5ad object. Please check your input and try again.

The weird thing is that https://github.com/chanzuckerberg/cellxgene/raw/main/example-dataset/pbmc3k.h5ad worked well.

Best,
Yoshi

[Fougere87]

@yyoshiaki Yes that's all ok, but as you are running the dockerfile from the repo which uses ubuntu:bionic (18.04 :-D) as a base image.
Therefore, in your docker env, you have python 3.6.
Try running
docker -it run -v "$PWD:/data/" -p 5005:5005 --entrypoint bash cellxgene
and then launch python to see the version.

@chryssiebrown have you checked your numba and h5py versions ? Are you launching cellxgene from docker or in your terminal ?

Best,
Chlo

[yyoshiaki]

@Fougere87 Thank you so much for your quick response.
I checked python and library versions by docker run -it -v "$PWD:/data/" -p 5005:5005 --entrypoint bash cellxgene.
Python 3.6.9, anndata==0.7.8, h5py==3.1.0 were installed.

By changing the base image from bionic to jammy, for example, I could fix the problem, #2628

Thank you,
Yoshi

[chryssiebrown]

That was very helpful - I had the newer version of python 3.9 but in my environment I was using python 3.6.9. I updated and that fixed the issue! Thanks all for your help, Chrys

…

On Aug 28, 2023, at 7:58 AM, Yoshiaki Yasumizu ***@***.***> wrote: @Fougere87 <https://github.com/Fougere87> Thank you so much for your quick response. I checked python and library versions by docker run -it -v "$PWD:/data/" -p 5005:5005 --entrypoint bash cellxgene. Python 3.6.9, anndata==0.7.8, h5py==3.1.0 were installed. By changing the base image from bionic to jammy, for example, I could fix the problem, #2628 <#2628> Thank you, Yoshi — Reply to this email directly, view it on GitHub <#2625 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOR6PHDLVQIULY3GKTREXW3XXSBVLANCNFSM6AAAAAA3S3VWAE>. You are receiving this because you were mentioned.

[chryssiebrown]

Hi, Unfortunately although that fixed the issue on my desktop, I am having the same issue on my MacBook, running cellxgene from the terminal. I have python 3.11.4 installed on my Mac. I also tried creating an environment with Python 3.9 and receive the same message as previously - I am still able to load older .5ad files, but not the recent ones. Thanks for your help, Chrys Error: File not found or is inaccessible. File must be an .h5ad object. Please check your input and try again.

…

On Aug 28, 2023, at 12:08 PM, Chrysothemis Brown ***@***.***> wrote: That was very helpful - I had the newer version of python 3.9 but in my environment I was using python 3.6.9. I updated and that fixed the issue! Thanks all for your help, Chrys > On Aug 28, 2023, at 7:58 AM, Yoshiaki Yasumizu ***@***.***> wrote: > > > @Fougere87 <https://github.com/Fougere87> Thank you so much for your quick response. > I checked python and library versions by docker run -it -v "$PWD:/data/" -p 5005:5005 --entrypoint bash cellxgene. > Python 3.6.9, anndata==0.7.8, h5py==3.1.0 were installed. > > By changing the base image from bionic to jammy, for example, I could fix the problem, #2628 <#2628> > Thank you, > Yoshi > > — > Reply to this email directly, view it on GitHub <#2625 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOR6PHDLVQIULY3GKTREXW3XXSBVLANCNFSM6AAAAAA3S3VWAE>. > You are receiving this because you were mentioned. >

[timslittle]

Chryssie I hope that you solved this issue, but in case it is helpful I was having similar problems despite up-to-date Python etc, and it turned out that the issue was that I was compressing the h5ad file in a way that Cellxgene couldn't recognise.