search

maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
102 stars 40 forks source link

alert:Could not load mouse_temp_atac/exprMatrix.bin?chr1|3115016|3115356, error undefined #242

Closed ckfromCN closed 2 years ago

ckfromCN commented 2 years ago

Hi, Thanks a lot for this amazing tool, I was trying to build my own sc-ATAC-seq browser and downloaded the already deployed data from https://cells.ucsc.edu/?ds=mouse-kidney-atac+atac to test it. But after I cbBuild, and searching for peek on the web expression, the web page alert me

Could not load mouse_temp_atac/exprMatrix.bin?chrX|164135350|164135896, error undefined

The same problem is repeated for the https://cells.ucsc.edu/?ds=fetal-chromatin-atlas+lung+peaks data image

data

https://cells.ucsc.edu/mouse-kidney-atac/atac/exprMatrix.tsv.gz https://cells.ucsc.edu/mouse-kidney-atac/atac/meta.tsv https://cells.ucsc.edu/mouse-kidney-atac/atac/UMAP.coords.tsv.gz

cellbrowser.cof

name="mouse_temp_atac"
shortLabel="atac"
exprMatrix="exprMatrix.tsv.gz"
meta="meta.tsv"
geneIdType="auto"
clusterField="clusters"
labelField="clusters"
enumFields=["pheno","clusters"]
coords=[{"file": "UMAP.coords.tsv", "shortLabel": "Seurat umap"}]
atacSearch = "mm10.gencode-M25"
geneLabel = "Peak"

OS/Platform

maximilianh commented 2 years ago

Hi, thanks for the feedback. On our website, I cannot reproduce this error, I search for Ace2 and I can select a peak. If I understood correctly, you cannot get this to work on your own mirror, but it's working on our website. It sounds as if something is different in your cellbrowser.conf config file.

One thing is not documented anywhere, but the data directories contain a copy of the original input configuration file in JSON format, here: https://cells.ucsc.edu/fetal-chromatin-atlas/lung/peaks/cellbrowser.json.bak. Does this help? E.g. the dataset fetal-chromatin-atlas/lung/peaks needs hg19 gene models, not mm10 ones. (but you may have used another dataset for the example here). There may also be other settings that are different than for your example.

If you want to "clone" a dataset onto your mirror, let us know, we should make this a lot easier and can give you rsync access to the original data directories.

On Thu, Apr 21, 2022 at 3:34 PM ckfromCN @.***> wrote:

Hi, Thanks a lot for this amazing tool, I was trying to build my own sc-ATAC-seq browser and downloaded the already deployed data from https://cells.ucsc.edu/?ds=mouse-kidney-atac+atac to test it. But after I cbBuild, and searching for peek on the web expression, the web page alert me

Could not load mouse_temp_atac/exprMatrix.bin?chrX|164135350|164135896, error undefined

The same problem is repeated for the https://cells.ucsc.edu/?ds=fetal-chromatin-atlas+lung+peaks data [image: image] https://user-images.githubusercontent.com/18496367/164467535-50e7b068-7caf-4374-a170-a664a07c47b4.png data

https://cells.ucsc.edu/mouse-kidney-atac/atac/exprMatrix.tsv.gz https://cells.ucsc.edu/mouse-kidney-atac/atac/meta.tsv https://cells.ucsc.edu/mouse-kidney-atac/atac/UMAP.coords.tsv.gz cellbrowser.cof

name="mouse_temp_atac"shortLabel="atac"exprMatrix="exprMatrix.tsv.gz"meta="meta.tsv"geneIdType="auto"clusterField="clusters"labelField="clusters"enumFields=["pheno","clusters"]coords=[{"file": "UMAP.coords.tsv", "shortLabel": "Seurat umap"}]atacSearch = "mm10.gencode-M25"geneLabel = "Peak"

OS/Platform

  • OS/Platform: centos7
  • cellBrowser version: 1.1.1
  • R :4.0.3
  • python :3.6.5

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/242, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TPQSRBUD6DUMDGLZM3VGFKM7ANCNFSM5T7ISRUA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

ckfromCN commented 2 years ago

Thank you for your support I really appreciate. Actually I used the hg19.gencode-28lift37 to run fetal-chromatin-atlas/lung/peaks ,but it has the same problem. I am building a database of singlecell data,and your project is important to me.It would be a great help to me if I could access the original data directories

ckfromCN commented 2 years ago

I tried again to create the file with cbBuild -o html -p 8888 and provide web services, this did not give an alert However, the html folder exported by cbBuild -o html is placed under tomcat webapps to provide web services, in this case there is an error (only ATAC peak data, scRNA data is normal)

maximilianh commented 2 years ago

Sorry there is no web service here, it’s all static files. Maybe that’s part of the misunderstanding?

But it’s great that the error went away, does this mean that we can close this issue ?

On Sat 23 Apr 2022 at 09:44, ckfromCN @.***> wrote:

I tried again to create the file with cbBuild -o html -p 8888 and provide web services, this did not give an alert However, the html folder exported by cbBuild -o html is placed under tomcat webapps to provide web services, in this case there is an error (only ATAC peak data, scRNA data is normal)

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/242#issuecomment-1107532371, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOJOGC5MBWTJ2Q56ALVGQSG7ANCNFSM5T7ISRUA . You are receiving this because you commented.Message ID: @.***>

ckfromCN commented 2 years ago

Yes, the problem was solved,I will close this issue later. May I ask how you deployed so many datasets under https://cells.ucsc.edu/? I find that using the cbBuild -p command to serve web pages seems to consume memory all the time

Sorry there is no web service here, it’s all static files. Maybe that’s part of the misunderstanding? But it’s great that the error went away, does this mean that we can close this issue ? … On Sat 23 Apr 2022 at 09:44, ckfromCN @.> wrote: I tried again to create the file with cbBuild -o html -p 8888 and provide web services, this did not give an alert However, the html folder exported by cbBuild -o html is placed under tomcat webapps to provide web services, in this case there is an error (only ATAC peak data, scRNA data is normal) — Reply to this email directly, view it on GitHub <#242 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOJOGC5MBWTJ2Q56ALVGQSG7ANCNFSM5T7ISRUA . You are receiving this because you commented.Message ID: @.>

maximilianh commented 2 years ago

Yes, sorry, don't use the built-in webserver for production services. It's just a small Python thing.

You can use any simple webserver that can serve static pages. Nginx, lighthttp, Apache or anything else. We use Apache.

On Sat, Apr 23, 2022 at 9:09 PM ckfromCN @.***> wrote:

Yes, the problem was solved,I will close this issue later. May I ask how you deployed so many datasets under https://cells.ucsc.edu/? I find that using the cbBuild -p command to serve web pages seems to consume memory all the time

Sorry there is no web service here, it’s all static files. Maybe that’s part of the misunderstanding? But it’s great that the error went away, does this mean that we can close this issue ? … <#m1150913607437535653> On Sat 23 Apr 2022 at 09:44, ckfromCN @.> wrote: I tried again to create the file with cbBuild -o html -p 8888 and provide web services, this did not give an alert However, the html folder exported by cbBuild -o html is placed under tomcat webapps to provide web services, in this case there is an error (only ATAC peak data, scRNA data is normal) — Reply to this email directly, view it on GitHub <#242 (comment) https://github.com/maximilianh/cellBrowser/issues/242#issuecomment-1107532371>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOJOGC5MBWTJ2Q56ALVGQSG7ANCNFSM5T7ISRUA https://github.com/notifications/unsubscribe-auth/AACL4TOJOGC5MBWTJ2Q56ALVGQSG7ANCNFSM5T7ISRUA . You are receiving this because you commented.Message ID: @.>

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/242#issuecomment-1107704924, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TK56CKYD5WM53CUETLVGTCNRANCNFSM5T7ISRUA . You are receiving this because you commented.Message ID: @.***>