Docker run too-many-cells error about too-many-cells HOT 22 CLOSED

What command did you use? What OS are you on?

from too-many-cells.

What command did you use? What OS are you on?

The command I used:
sudo docker run -m 5000000 -it --rm -v "/Users/lijia/Downloads/too-many-cells/" -v "/usr/local/bin" gregoryschwartz/too-many-cells:0.2.2.0 make-tree --matrix-path Veh.matrix.csv --labels-file labels.csv --draw-collection "PieRing" --output out

I am using macOS high Sierra version 10.13.6

Thanks

from too-many-cells.

Why /usr/local/bin? That might be playing with the R in the docker container. What if you omit that?

from too-many-cells.

from too-many-cells.

What stage does it fail? Does it work for other data?

from too-many-cells.

from too-many-cells.

What if you try the workshop (https://gregoryschwartz.github.io/too-many-cells/workshop/workshop.html)?

from too-many-cells.

I asked other people in our lab to test Docker run too-many-cells, they also have the same error.

from too-many-cells.

What if you try the workshop (https://gregoryschwartz.github.io/too-many-cells/workshop/workshop.html)?

I tried workshop under Catalina and High Sierra, both have the following errors:

While building package cairo-0.13.5.0 using:
/private/var/folders/xh/k7b18vjx6kz051t7q29r8mfsp28xc5/T/stack75478/cairo-0.13.5.0/.stack-work/dist/x86_64-osx/Cabal-2.2.0.1/setup/setup --builddir=.stack-work/dist/x86_64-osx/Cabal-2.2.0.1 configure --user --package-db=clear --package-db=global --package-db=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/pkgdb --libdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/lib --bindir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/bin --datadir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/share --libexecdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/libexec --sysconfdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/etc --docdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/cairo-0.13.5.0 --htmldir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/cairo-0.13.5.0 --haddockdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/cairo-0.13.5.0 --dependency=Cabal=Cabal-2.2.0.1 --dependency=array=array-0.5.2.0 --dependency=base=base-4.11.1.0 --dependency=bytestring=bytestring-0.10.8.2 --dependency=gtk2hs-buildtools=gtk2hs-buildtools-0.13.4.0-BeTuALJn73yF2BRI2iGnJc --dependency=mtl=mtl-2.2.2 --dependency=text=text-1.2.3.0 --dependency=utf8-string=utf8-string-1.0.1.1-LRSjvSC6FZkKPp48Qszoj8 -fcairo_pdf -fcairo_ps -fcairo_svg --exact-configuration --ghc-option=-fhide-source-paths
Process exited with code: ExitFailure 1

-- While building package inline-r-0.9.2 using:
/Users/jli/.stack/setup-exe-cache/x86_64-osx/Cabal-simple_mPHDZzAJ_2.2.0.1_ghc-8.4.3 --builddir=.stack-work/dist/x86_64-osx/Cabal-2.2.0.1 configure --user --package-db=clear --package-db=global --package-db=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/pkgdb --libdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/lib --bindir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/bin --datadir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/share --libexecdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/libexec --sysconfdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/etc --docdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/inline-r-0.9.2 --htmldir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/inline-r-0.9.2 --haddockdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/inline-r-0.9.2 --dependency=aeson=aeson-1.4.0.0-EAbp2GiwrvTH27nXdJzV0g --dependency=base=base-4.11.1.0 --dependency=bytestring=bytestring-0.10.8.2 --dependency=containers=containers-0.5.11.0 --dependency=data-default-class=data-default-class-0.1.2.0-2kYzERBLX3wJoPfj7mwVvW --dependency=deepseq=deepseq-1.4.3.0 --dependency=exceptions=exceptions-0.10.0-DmsI5QMvE6e6QgVkMINEKb --dependency=inline-c=inline-c-0.6.1.0-FM9gF7RqOpoLWRlok3Pud0 --dependency=mtl=mtl-2.2.2 --dependency=pretty=pretty-1.1.3.6 --dependency=primitive=primitive-0.6.3.0-DaZpcxwJp2TGn8ITSgfI4C --dependency=process=process-1.6.3.0 --dependency=reflection=reflection-2.1.4-ET4Qfoy5lmWBopRK3ezJIQ --dependency=setenv=setenv-0.1.1.3-H1xmIqlPy4yIDquO6eJhBl --dependency=singletons=singletons-2.4.1-FDzlisNNwplIrNjegYYDdD --dependency=template-haskell=template-haskell-2.13.0.0 --dependency=text=text-1.2.3.0 --dependency=th-lift=th-lift-0.7.10-88ozaMeoe8eDZSlyIjheFa --dependency=th-orphans=th-orphans-0.13.6-6mvRAE1wQLBDXpoe3PtgV3 --dependency=transformers=transformers-0.5.5.0 --dependency=unix=unix-2.7.2.2 --dependency=vector=vector-0.12.0.1-GGZqQZyzchy8YFPCF67wxL --exact-configuration --ghc-option=-fhide-source-paths
Process exited with code: ExitFailure 1

-- While building package glib-0.13.8.0 using:
/private/var/folders/xh/k7b18vjx6kz051t7q29r8mfsp28xc5/T/stack75478/glib-0.13.8.0/.stack-work/dist/x86_64-osx/Cabal-2.2.0.1/setup/setup --builddir=.stack-work/dist/x86_64-osx/Cabal-2.2.0.1 configure --user --package-db=clear --package-db=global --package-db=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/pkgdb --libdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/lib --bindir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/bin --datadir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/share --libexecdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/libexec --sysconfdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/etc --docdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/glib-0.13.8.0 --htmldir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/glib-0.13.8.0 --haddockdir=/Users/jli/.stack/snapshots/x86_64-osx/d96d1c41d18571a54eb85ebae848040464e1476263180e538beb77700203aeb1/8.4.3/doc/glib-0.13.8.0 --dependency=Cabal=Cabal-2.2.0.1 --dependency=base=base-4.11.1.0 --dependency=bytestring=bytestring-0.10.8.2 --dependency=containers=containers-0.5.11.0 --dependency=gtk2hs-buildtools=gtk2hs-buildtools-0.13.4.0-BeTuALJn73yF2BRI2iGnJc --dependency=text=text-1.2.3.0 --dependency=utf8-string=utf8-string-1.0.1.1-LRSjvSC6FZkKPp48Qszoj8 -fclosure_signals --exact-configuration --ghc-option=-fhide-source-paths
Process exited with code: ExitFailure 1
Progress 8/45

from too-many-cells.

You should use docker with the workshop in your case.

from too-many-cells.

Is it possible that you are not giving docker enough memory? -m 16g or higher? Also, did you try a small toy example of like 5 cells with 5 genes or something like that?

from too-many-cells.

from too-many-cells.

You are telling docker to mount /Users/lijia/Downloads to that location in the container, but pointing to a file in / in the container. So try:

sudo docker run -m 16g -it --rm -v "/Users/lijia/Downloads/:/Users/lijia/Downloads" gregoryschwartz/too-many-cells:0.2.2.0 make-tree --matrix-path /Users/lijia/Downloads/too-many-cells/test.matrix.csv --labels-file /Users/lijia/Downloads/too-many-cells/test.label.csv --draw-collection "PieRing" --output /Users/lijia/Downloads/too-many-cells/out

from too-many-cells.

You are telling docker to mount /Users/lijia/Downloads to that location in the container, but pointing to a file in / in the container. So try:

sudo docker run -m 16g -it --rm -v "/Users/lijia/Downloads/:/Users/lijia/Downloads" gregoryschwartz/too-many-cells:0.2.2.0 make-tree --matrix-path /Users/lijia/Downloads/too-many-cells/test.matrix.csv --labels-file /Users/lijia/Downloads/too-many-cells/test.label.csv --draw-collection "PieRing" --output /Users/lijia/Downloads/too-many-cells/out

Thank you! I can run it successfully.

from too-many-cells.

For your own data you probably need to either up the memory, mount it like you did here, or both.

from too-many-cells.

Hi again Dr. Schwartz... I now ran into the same problem as @lijiacd985 did...
I followed the instructions you suggested according to the communications above but the problem remains.

Here is my command:
sudo docker run -m 16g -it --rm -v "/d/Users/zeiss/tmcdocker/:/d/Users/zeiss/tmcdocker"
gregoryschwartz/too-many-cells:0.2.2.0 make-tree
--matrix-path /d/Users/zeiss/tmcdocker/data/brain/filtered_feature_bc_matrix/
--matrix-path /d/Users/zeiss/tmcdocker/data/heart/filtered_feature_bc_matrix/
--output /d/Users/zeiss/tmcdocker/out

Error messages:
Loading matrix [....................................................] 0%
too-many-cells:
Matrix path does not exist.
CallStack (from HasCallStack):
error, called at app/Main.hs:273:36 in main:Main

Config.:
I am using the Docker Toolbox on a Windows 7 computer.
Testing with the brain+heart data set you used in your workshop.
The current path is: /d/Users/zeiss/tmcdocker/

Looking forward to your suggestions!

Regards,
Joey

from too-many-cells.

@joyeblog Is this after you got it to work with other data? If not, then check that Windows has permissions to mount in your docker Settings under Shared Drives (or the like). Also, silly question, but your Windows mount point looks like a Unix directory, not Windows, is this correct?

from too-many-cells.

@GregorySchwartz No, I have not tried my own data yet. I was thinking to replicate your workshop results first to ensure there isn't any technical errors before moving on to my sequencing dataset.

Everything is run in the Oracle Virtual Box, I gave the permission to mount on D:\Users\zeiss\tmcdocker according to the instructions from my issue #26 . Please see the attached screenshot from the Oracle Virtual Box.

Interesting question... Is the path format for Windows different from the one I had above? I tried the following command (Windows format path):
sudo docker run -m 16g -it --rm -v "D:/Users/zeiss/tmcdocker:/D:/Users/zeiss/tmcdocker"
gregoryschwartz/too-many-cells:0.2.2.0 make-tree
--matrix-path /D:/Users/zeiss/tmcdocker/data/brain/filtered_feature_bc_matrix/

And got error message:
Error response from daemon: invalid volume specification: 'D:/Users/zeiss/tmcdocker:/D:/Users/zeiss/tmcdocker'. See 'docker run --help'.

Sorry for keep bothering you with basic and silly questions.. Thanks for your time!

@joyeblog Is this after you got it to work with other data? If not, then check that Windows has permissions to mount in your docker Settings under Shared Drives (or the like). Also, silly question, but your Windows mount point looks like a Unix directory, not Windows, is this correct?

from too-many-cells.

In the volume argument, before the : is the host and after is the container. The container has a linux filesystem, so you don't want to repeat the invalid path. So you should have that first part, but change the second to whatever you want and have another volume argument pointing to the output folder on the container mapped to the host.

from too-many-cells.

Thanks again for the quick response! Honestly it sounds a bit too technical for me. Would you please use an example? Let's say,
The current path on docker-machine: /home/docker
The current path mounted on the Windows system: D:/Users/zeiss/tmcdocker
The folder I want all the output files in is also: D:/Users/zeiss/tmcdocker

In this case, what exactly should I write inside the quotation mark below?
sudo docker run -m 16g -it --rm -v "???"
gregoryschwartz/too-many-cells:0.2.2.0 make-tree
--matrix-path ./data/brain/filtered_feature_bc_matrix/
--matrix-path ./data/heart/filtered_feature_bc_matrix/
--output out

Thanks,
Joey

In the volume argument, before the : is the host and after is the container. The container has a linux filesystem, so you don't want to repeat the invalid path. So you should have that first part, but change the second to whatever you want and have another volume argument pointing to the output folder on the container mapped to the host.

from too-many-cells.

I don't know what your file system looks like, but maybe something like

-v "D:/Users/zeiss/tmcdocker:/work"
gregoryschwartz/too-many-cells:0.2.2.0 make-tree
--matrix-path /work/data/brain/filtered_feature_bc_matrix/
--matrix-path /work/data/heart/filtered_feature_bc_matrix/
--output /work/out

from too-many-cells.

Thanks a lot! I will give a try.

from too-many-cells.