Terra-PANOPLY startup notebook does not populate data tab
Hi all,
I am trying to run a jupyter notebook in the PANOPLY tutorial workspace (PANOPLY_Production_Pipelines_v1_0), according to the instructions in the PANOPLY github repository.
The notebook is supposed to take a zip file uploaded manually to the files section under the data tab and then populate the tables. I manage to run the notebook smoothly but the data tab does not get populated when it's done.
Looking at the jupyter logs I see the following error:
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copy input files to Terra -
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CommandException: "cp" command does not support provider-only URLs.
Thanks in advance for you help!
Gali
Comments
10 comments
Hi Gali Arad,
Thanks for writing in. We'll take a look at your question and get back to you as soon as we can. Please note, our responses may be delayed due to limited support staff during the pre-holiday week.
Thank you for your patience and understanding.
Best,
Samantha
Hi Gali Arad,
Can you share the workspace where you are seeing this issue with Terra-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
Please provide us with a link to your workspace. We’ll be happy to take a closer look as soon as we can!
Kind regards,
Samantha
Thank you for the quick response! I just shared the workspace.
Hi Gali Arad,
Can you share a link to your workspace? Also, if the workspace is protected by an authorization domain, please add me (svelasqu@broadinstitute.org) to that authorization domain so I can access the workspace.
Best,
Samantha
Hi Samantha,
I added you to the authorization domain, and this would be the link to the workspace: https://app.terra.bio/#workspaces/terra-protai2/PANOPLY_Production_Pipelines_v1_0_protai_2
Thanks
Gali
Hi Gali Arad,
Can you share your Jupyter log file? I'm afraid this might be an issue with the functions being used in the notebook, which Terra Support does not own or maintain. However, I can get in touch with the owners of the PANOPLY_Tutorial workspace and get their opinion.
Best,
Samantha
See the log file contents below.
I also suspect the problem might be with the config.yaml file generated by the notebook.
It contains these parameters and values:
globals:
project: broad-firecloud-cptac
group: GROUP_Broad_CPTAC@firecloud.org
meth_space: broadcptac
And I think maybe the group should be = Protai_Group@firecloud.org and project should be = terra-protai2 (the project and group I am part of)?
As for the log file - couldn't attach a file but see the log text here:
---------------------------
splitting input data-------
---------------------------
running
'/usr/lib/R/bin/R --slave --no-restore --file=/panda/bin/r-source/split.r --args -e gct -i pipeline-input/PANOPLY_Production_Pipelines_v1_0_protai_2-rna.gct -d rna -o split-data/rna'
parsing as GCT v1.3
pipeline-input/PANOPLY_Production_Pipelines_v1_0_protai_2-rna.gct 15800 rows, 77 cols, 1 row descriptors, 13 col descriptors
Saving file to split-data/rna/AO.A12D.01TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A131.01TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A12B.01TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A18Q.02TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A130.02TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A138.03TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/E2.A154.03TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A12L.04TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0EX.04TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AN.A04A.05TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0AV.05TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A12T.06TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A8.A06Z.07TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0CM.07TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A18U.08TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0EQ.08TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A0U4.09TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0J9.10TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A1AP.11TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AN.A0FK.11TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0J6.11TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A7.A13F.12TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0E1.12TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A7.A0CE.13TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0YC.13TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0JC.14TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A8.A08Z.14TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A0TX.14TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A8.A076.15TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A126.15TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0C1.16TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0EY.16TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A1AW.17TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A1AV.17TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A135.17TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0EV.18TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AN.A0AM.18TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/D8.A142.18TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AN.A0FL.19TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0DG.19TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A0TV.20TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A12Z.20TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0JJ.20TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0JE.21TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AN.A0AJ.21TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A7.A0CJ.22TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A12F.22TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A8.A079.23TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0T3.24TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0YD.24TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A0TR.25TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A03O.25TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A12E.26TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A8.A06N.26TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0YG.27TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A18N.27TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AN.A0AL.28TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0T6.29TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/E2.A158.29TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/E2.A15A.29TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0JM.30TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A12V.30TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0D2.31TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A12U.31TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A1AS.31TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A8.A09G.32TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/C8.A134.32TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0YF.33TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0DD.33TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0E9.33TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AR.A0TT.34TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0SW.35TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/AO.A0JL.35TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0BV.35TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0YM.36TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/BH.A0C7.36TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
Saving file to split-data/rna/A2.A0SX.36TCGA-rna.gct
Dimensions of matrix: [15800x1]
Setting precision to 4
Saved.
There were 50 or more warnings (use warnings() to see the first 50)
---------------------------
copy input files to Terra -
---------------------------
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
CommandException: "cp" command does not support provider-only URLs.
Hi, hope you enjoyed the festive season!
It would be great if you could kindly update me about the status of the error discussed here before the holidays.
Many thanks and happy 2022!
Gali
Hi Gali Arad,
Happy New Year! I reached out to the owner of the PANOPLY workspace and they confirmed that the issue you are seeing is due to a bug that they are currently looking into. I will let you know once I hear back about the bug being resolved.
Best,
Samantha
Hi Gali Arad,
I have just received word that this issue has been resolved. A new docker has been created (broadcptac/panda:1_01) that should fix the issue and correctly deal with using the appropriate workspace project. The main PANOPLY workspaces have been updated accordingly: (PANOPLY_Production_Pipelines_v1_0 and PANOPLY_Production_Modules_v1_0).
Best,
Samantha
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