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[scATAC-seq]ERROR:root:Cannot download hg38.gencode-34.json #232

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ckfromCN opened this issue Dec 16, 2021 · 10 comments
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[scATAC-seq]ERROR:root:Cannot download hg38.gencode-34.json #232

ckfromCN opened this issue Dec 16, 2021 · 10 comments

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@ckfromCN
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Hi, I am trying to set up my own sc-ATAC-seq browser from https://cells.ucsc.edu/?ds=cortex-atac+peaks and I have a few questions.

  1. When I build an html webpage, the program was interrupted and reminded me that the json file could not be downloaded

ERROR:root:Cannot download https://cells.ucsc.edu/downloads/cellbrowserData/genes/hg38.gencode-34.json

then I check your website https://cells.ucsc.edu/downloads/cellbrowserData/genes/ there are not such file.
How can I solve this problem?

  1. You mentioned that we need a required file Expression matrix with cell names as columns and peak ranges as rows. Does the row name of this expression matrix require gene names or chromosome regions?

  2. I want to set up another scATAC-seq data from the mm9 reference genome. I observed that your website https://cells.ucsc.edu/downloads/cellbrowserData/genes/ does not have such a file, how can I get such a file.

Here are some detail .

OS/Platform

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

cellbrowser.conf

name = "sample"
shortLabel="sample"
exprMatrix="exprMatrix.tsv.gz"
geneIdType="gencode34"
meta="meta.tsv"
coords=[
    {"file":"UMAP.coords.tsv", "shortLabel":"umap"},
    {"file":"PFCV1_subset_UMAP.coords.tsv", "shortLabel":"PFCV1_subset_UMAP"}
]
clusterField="CellType"
radius = 5
alpha = 0.3
atacSearch = "hg38.gencode-34" # Version downloaded in Step 3 combined with the UCSC assembly name
geneLabel = "Peak"

command

# download peak matrix  by wget from `https://cells.ucsc.edu/?ds=cortex-atac+peaks`
cbTools mtx2tsv matrix.mtx.gz features.tsv.gz barcodes.tsv.gz exprMatrix.tsv.gz

cbBuild -o html

Detailed error message

ERROR:root:Cannot download https://cells.ucsc.edu/downloads/cellbrowserData/genes/hg38.gencode-34.
INFO:root:Syncing [None] to html/genes
ERROR:root:Unexpected error: (<class 'TypeError'>, TypeError('expected str, bytes or os.PathLike object, not NoneType',), <traceback object at 0x7f02edc3a908>)
Traceback (most recent call last):
  File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 4783, in cbBuildCli
    build(confFnames, outDir, port, redo=options.redo)
  File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 4599, in build
    copyGenes(inConf, outConf, outDir)
  File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 3894, in copyGenes
    syncFiles([inFname], geneDir)
  File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 2781, in syncFiles
    outFname = join(outDir, basename(inFname))
  File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/posixpath.py", line 146, in basename
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType
@maximilianh
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maximilianh commented Dec 16, 2021 via email

@maximilianh
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maximilianh commented Dec 16, 2021 via email

@maximilianh
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maximilianh commented Dec 16, 2021 via email

@ckfromCN
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Thanks for your reply, it has bothered me for a long time

I have tried this command, and it passed.

However, when I set it in tomcat, the webpage cannot display umap and reports
Internal error: If the coordinates have not been set, it cannot be drawn
This is my latest cellbrowser.conf

name = "sample"
shortLabel="sample"
exprMatrix="exprMatrix.tsv.gz"
geneIdType="auto"
meta="meta.tsv"
coords=[
    {"file":"UMAP.coords.tsv", "shortLabel":"umap"},
    {"file":"PFCV1_subset_UMAP.coords.tsv", "shortLabel":"PFCV1_subset_UMAP"}
]
clusterField="CellType"
radius = 5
alpha = 0.3
atacSearch = "hg38.gencode-34" # Version downloaded in Step 3 combined with the UCSC assembly name
geneLabel = "Peak"

BTW,how can I build a mm9.json like hg38.gencode-34.json ?

Thanks again.

Oops, sorry I meant this command: $ cbGenes build hg38 gencode-34 On Thu, Dec 16, 2021 at 2:45 PM Maximilian Haeussler @.> wrote:
…
Thank you for this detailed error report. This is an oversight on our side. I'll fix this ASAP and push the .json files to the public site for gencode-34. In the meantime you can run this command to fix the problem: $ cbGenes build hg38.gencode-34 Please let me know if it worked, we can close the ticket then. On Thu, Dec 16, 2021 at 4:57 AM ckfromCN @.> wrote: > Hi, I am trying to set up my own sc-ATAC-seq browser from > https://cells.ucsc.edu/?ds=cortex-atac+peaks and I have a few questions. > > 1. When I build an html webpage, the program was interrupted and > reminded me that the json file could not be downloaded > > ERROR:root:Cannot download > https://cells.ucsc.edu/downloads/cellbrowserData/genes/hg38.gencode-34.json > > then I check your website > https://cells.ucsc.edu/downloads/cellbrowserData/genes/ there are not > such file. > How can I solve this problem? > > 1. > > You mentioned that we need a required file Expression matrix with > cell names as columns and peak ranges as rows. Does the row name of > this expression matrix require gene names or chromosome regions? > 2. > > I want to set up another scATAC-seq data from the mm9 reference > genome. I observed that your website > https://cells.ucsc.edu/downloads/cellbrowserData/genes/ does not have > such a file, how can I get such a file. > > Here are some detail . > OS/Platform > > - OS/Platform: centos7 > - cellBrowser version: 1.1.1 > - R :4.0.3 > - python :3.6.5 > > cellbrowser.conf > > name = "sample"shortLabel="sample"exprMatrix="exprMatrix.tsv.gz"geneIdType="gencode34"meta="meta.tsv"coords=[ > {"file":"UMAP.coords.tsv", "shortLabel":"umap"}, > {"file":"PFCV1_subset_UMAP.coords.tsv", "shortLabel":"PFCV1_subset_UMAP"} > ]clusterField="CellType"radius = 5alpha = 0.3atacSearch = "hg38.gencode-34" # Version downloaded in Step 3 combined with the UCSC assembly namegeneLabel = "Peak" > > command > > # download peak matrix by wget from [https://cells.ucsc.edu/?ds=cortex-atac+peaks](https://cells.ucsc.edu/?ds=cortex-atac+peaks%60) https://cells.ucsc.edu/?ds=cortex-atac+peaks > cbTools mtx2tsv matrix.mtx.gz features.tsv.gz barcodes.tsv.gz exprMatrix.tsv.gz > > cbBuild -o html > > Detailed error message > > ERROR:root:Cannot download https://cells.ucsc.edu/downloads/cellbrowserData/genes/hg38.gencode-34. > INFO:root:Syncing [None] to html/genes > ERROR:root:Unexpected error: (<class 'TypeError'>, TypeError('expected str, bytes or os.PathLike object, not NoneType',), <traceback object at 0x7f02edc3a908>) > Traceback (most recent call last): > File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 4783, in cbBuildCli > build(confFnames, outDir, port, redo=options.redo) > File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 4599, in build > copyGenes(inConf, outConf, outDir) > File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 3894, in copyGenes > syncFiles([inFname], geneDir) > File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 2781, in syncFiles > outFname = join(outDir, basename(inFname)) > File "/home/kchen/anaconda2/envs/singlecell/lib/python3.6/posixpath.py", line 146, in basename > p = os.fspath(p) > TypeError: expected str, bytes or os.PathLike object, not NoneType > > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#232>, or unsubscribe > https://github.com/notifications/unsubscribe-auth/AACL4TLKZLFE62AHG4N6L4DURFPSHANCNFSM5KFIUNNA > . > Triage notifications on the go with GitHub Mobile for iOS > https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 > or Android > https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. > >

@maximilianh
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Hi, sorry for the long delay, christmas got in the way.

I don't know what you mean with "Tomcat", are you sure that cellbrowsers can be served from your Tomcat server? For me, that's a Java server and may not have byte range requests. Were you able to serve the mini demo from your Tomcat?

@ckfromCN
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ckfromCN commented Jan 4, 2022

Hi, sorry for the long delay, christmas got in the way.

I don't know what you mean with "Tomcat", are you sure that cellbrowsers can be served from your Tomcat server? For me, that's a Java server and may not have byte range requests. Were you able to serve the mini demo from your Tomcat?

Yes, I put the cbBuild exported html directory in tomcat's webapp directory and run it, the web page shows the same result as cbBuild -o html -p 8888, I think the reason for the web page error Internal error: If the coordinates have not been set, it cannot be drawnshould not be related to tomcat

@maximilianh
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maximilianh commented Jan 5, 2022 via email

@ckfromCN
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Can you share the public URL of this directory? If not: I'm pretty sure that we have had this error message come up before. I could well be related to your Tomcat... It could also be due to something related to your cellbrowser.conf file. Can you share this file here, at least the lines where the "coords" cell coordinates are defined?
…
On Tue, Jan 4, 2022 at 3:53 AM ckfromCN @.> wrote: Hi, sorry for the long delay, christmas got in the way. I don't know what you mean with "Tomcat", are you sure that cellbrowsers can be served from your Tomcat server? For me, that's a Java server and may not have byte range requests. Were you able to serve the mini demo from your Tomcat? Yes, I put the cbBuild exported html directory in tomcat's webapp directory and run it, the web page shows the same result as cbBuild -o html -p 8888, I think the reason for the web page error Internal error: If the coordinates have not been set, it cannot be drawnshould not be related to tomcat — Reply to this email directly, view it on GitHub <#232 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TLDF7RAZTVAT3TFNH3UUJOI3ANCNFSM5KFIUNNA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.Message ID: @.>

Here are some documents you may need, you can also view this issue by visiting http://101.34.228.19:8097/sc-atac
scATAC_conf.zip

@maximilianh
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Oh boy, I have a hard time with this. I know that the file with the midpoints of the labels hasn't been generated. But I don't know why that would be the case... can I get a copy of the input files? If I have the input files, so the tsv.gz etc and the cellbrowser.conf, I can try to reproduce it and can debug it here... is that OK?

@maximilianh
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maximilianh commented Apr 21, 2022 via email

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@maximilianh @ckfromCN