Issue w/ running cbSeurat: argument "counts" is missing, with no default #265
Comments
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Hm yes I don’t think I’ve tested on Seurat. Do you want share your matrix ?
Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4 ?
…On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
Hi,
I’ve been building my cellbrowsers for matrix files for a while now and
was working fine but after some update the pipeline doesn’t seem to be
working any more.
I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
features.tsv.gz to the cellbrowser by first building the exprMatrix.tsv.gz
using “cbTool mtx2tsv …” and that step seem to work but then next step
cbSeurat is failing.
Any idea what can be the problem? Is it a problem of using Seurat 5.0.0 w/
latest version of cellbrowser?
Thanks!
Alejandro.
------------------------------
cbSeurat --exprMatrix=exprMatrix.tsv.gz
--outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
INFO:root:Wrote R script to
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
through Rscript
Seurat loaded, version 5.0.0
[1] "Seurat: Reading data"
[1] "Seurat: Reading data"
[1] "Loading input data matrix"
[1] "Loading tsv file with read.delim"
[1] "Seurat: Setup"
Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes =
200) :
argument "counts" is missing, with no default
Execution halted
real 1m33.191s
user 1m17.847s
sys 0m1.896s
INFO:root:Wrote logfile of R run to
/var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
ERROR:root:R script did not complete successfully. Check
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and analysisLog.txt.
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Hi….The problem is that I’m having a lot of errors when trying to install Seurat 3 or 4. I was able to do it before but seem like it’s failing now.
Question: Is there a way of going from the matrix.mtx, features.tsv and barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
Thanks!
Alejandro.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Thursday, November 30, 2023 at 11:59 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Hm yes I don’t think I’ve tested on Seurat. Do you want share your matrix ?
Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4 ?
On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
Hi,
I’ve been building my cellbrowsers for matrix files for a while now and
was working fine but after some update the pipeline doesn’t seem to be
working any more.
I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
features.tsv.gz to the cellbrowser by first building the exprMatrix.tsv.gz
using “cbTool mtx2tsv …” and that step seem to work but then next step
cbSeurat is failing.
Any idea what can be the problem? Is it a problem of using Seurat 5.0.0 w/
latest version of cellbrowser?
Thanks!
Alejandro.
------------------------------
cbSeurat --exprMatrix=exprMatrix.tsv.gz
--outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
INFO:root:Wrote R script to
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
through Rscript
Seurat loaded, version 5.0.0
[1] "Seurat: Reading data"
[1] "Seurat: Reading data"
[1] "Loading input data matrix"
[1] "Loading tsv file with read.delim"
[1] "Seurat: Setup"
Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes =
200) :
argument "counts" is missing, with no default
Execution halted
real 1m33.191s
user 1m17.847s
sys 0m1.896s
INFO:root:Wrote logfile of R run to
/var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
ERROR:root:R script did not complete successfully. Check
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and analysisLog.txt.
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Wait... why are you running Seurat? you're running cbSeurat, Sorry I
didn't see that, I was convinced that you're using cbImportSeurat.
I haven't tested cbSeurat in a long time! I should probably retire it.
Don't you have umap coordinates etc as tsv files? If so, you can go
directly to cbBuild.
If you need UMAP coords and clustering and cluster markers, and these
things are not already there in the meta or separate tsv files, you can
also use cbScanpy, which at this point has had a ton more testing.
…On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
Hi….The problem is that I’m having a lot of errors when trying to install
Seurat 3 or 4. I was able to do it before but seem like it’s failing now.
Question: Is there a way of going from the matrix.mtx, features.tsv and
barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
Thanks!
Alejandro.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Thursday, November 30, 2023 at 11:59 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Hm yes I don’t think I’ve tested on Seurat. Do you want share your matrix
?
Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4 ?
On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> Hi,
> I’ve been building my cellbrowsers for matrix files for a while now and
> was working fine but after some update the pipeline doesn’t seem to be
> working any more.
> I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> features.tsv.gz to the cellbrowser by first building the
exprMatrix.tsv.gz
> using “cbTool mtx2tsv …” and that step seem to work but then next step
> cbSeurat is failing.
> Any idea what can be the problem? Is it a problem of using Seurat 5.0.0
w/
> latest version of cellbrowser?
> Thanks!
> Alejandro.
> ------------------------------
>
> cbSeurat --exprMatrix=exprMatrix.tsv.gz
> --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> INFO:root:Wrote R script to
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> through Rscript
> Seurat loaded, version 5.0.0
> [1] "Seurat: Reading data"
> [1] "Seurat: Reading data"
> [1] "Loading input data matrix"
> [1] "Loading tsv file with read.delim"
> [1] "Seurat: Setup"
> Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes =
> 200) :
> argument "counts" is missing, with no default
> Execution halted
>
> real 1m33.191s
> user 1m17.847s
> sys 0m1.896s
> INFO:root:Wrote logfile of R run to
> /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> ERROR:root:R script did not complete successfully. Check
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
analysisLog.txt.
>
> —
> Reply to this email directly, view it on GitHub
> <#265><
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Hi…Thanks again for your response. I’m trying to setup a somehow generic process where I take a set of matrix.mtx, features.tsv and barcodes.tsv files and visualize them w/ the cellbrowser.
I’m not sure if that contains the UMAP coords and clustering or of they always will so that’s why I thought I had to go thru’ Seurat but if not needed and you can point me to an example on how to go directly to the cellbrowser I’d really appreciate.
In the meantime I’ll try to see if I can get the cbScanpy to work w/ these files!
Thanks!
Alejandro.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 6:53 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Wait... why are you running Seurat? you're running cbSeurat, Sorry I
didn't see that, I was convinced that you're using cbImportSeurat.
I haven't tested cbSeurat in a long time! I should probably retire it.
Don't you have umap coordinates etc as tsv files? If so, you can go
directly to cbBuild.
If you need UMAP coords and clustering and cluster markers, and these
things are not already there in the meta or separate tsv files, you can
also use cbScanpy, which at this point has had a ton more testing.
On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
Hi….The problem is that I’m having a lot of errors when trying to install
Seurat 3 or 4. I was able to do it before but seem like it’s failing now.
Question: Is there a way of going from the matrix.mtx, features.tsv and
barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
Thanks!
Alejandro.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Thursday, November 30, 2023 at 11:59 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Hm yes I don’t think I’ve tested on Seurat. Do you want share your matrix
?
Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4 ?
On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> Hi,
> I’ve been building my cellbrowsers for matrix files for a while now and
> was working fine but after some update the pipeline doesn’t seem to be
> working any more.
> I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> features.tsv.gz to the cellbrowser by first building the
exprMatrix.tsv.gz
> using “cbTool mtx2tsv …” and that step seem to work but then next step
> cbSeurat is failing.
> Any idea what can be the problem? Is it a problem of using Seurat 5.0.0
w/
> latest version of cellbrowser?
> Thanks!
> Alejandro.
> ------------------------------
>
> cbSeurat --exprMatrix=exprMatrix.tsv.gz
> --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> INFO:root:Wrote R script to
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> through Rscript
> Seurat loaded, version 5.0.0
> [1] "Seurat: Reading data"
> [1] "Seurat: Reading data"
> [1] "Loading input data matrix"
> [1] "Loading tsv file with read.delim"
> [1] "Seurat: Setup"
> Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes =
> 200) :
> argument "counts" is missing, with no default
> Execution halted
>
> real 1m33.191s
> user 1m17.847s
> sys 0m1.896s
> INFO:root:Wrote logfile of R run to
> /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> ERROR:root:R script did not complete successfully. Check
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
analysisLog.txt.
>
> —
> Reply to this email directly, view it on GitHub
> <#265><<https://urldefense.us/v2/url?u=https-3A__github.com_maximilianh_cellBrowser_issues_265-253E-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=WEOTMuUcsGyzckemOLLWcDzp95SJ2csSRDbvikiPTLWi_RLwW07n9W7lipWmOvlJ&s=dd1olCyAG3B3qPBBeNK0wQMCSkPDrD227KBxN6PecUs&e=>
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Yes try cbScanpy ! It does exactly that !
…On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
Hi…Thanks again for your response. I’m trying to setup a somehow generic
process where I take a set of matrix.mtx, features.tsv and barcodes.tsv
files and visualize them w/ the cellbrowser.
I’m not sure if that contains the UMAP coords and clustering or of they
always will so that’s why I thought I had to go thru’ Seurat but if not
needed and you can point me to an example on how to go directly to the
cellbrowser I’d really appreciate.
In the meantime I’ll try to see if I can get the cbScanpy to work w/ these
files!
Thanks!
Alejandro.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 6:53 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Wait... why are you running Seurat? you're running cbSeurat, Sorry I
didn't see that, I was convinced that you're using cbImportSeurat.
I haven't tested cbSeurat in a long time! I should probably retire it.
Don't you have umap coordinates etc as tsv files? If so, you can go
directly to cbBuild.
If you need UMAP coords and clustering and cluster markers, and these
things are not already there in the meta or separate tsv files, you can
also use cbScanpy, which at this point has had a ton more testing.
On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> Hi….The problem is that I’m having a lot of errors when trying to
install
> Seurat 3 or 4. I was able to do it before but seem like it’s failing
now.
> Question: Is there a way of going from the matrix.mtx, features.tsv and
> barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
>
> Thanks!
> Alejandro.
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Thursday, November 30, 2023 at 11:59 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Hm yes I don’t think I’ve tested on Seurat. Do you want share your
matrix
> ?
> Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4 ?
>
> On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
>
> > Hi,
> > I’ve been building my cellbrowsers for matrix files for a while now
and
> > was working fine but after some update the pipeline doesn’t seem to be
> > working any more.
> > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > features.tsv.gz to the cellbrowser by first building the
> exprMatrix.tsv.gz
> > using “cbTool mtx2tsv …” and that step seem to work but then next step
> > cbSeurat is failing.
> > Any idea what can be the problem? Is it a problem of using Seurat
5.0.0
> w/
> > latest version of cellbrowser?
> > Thanks!
> > Alejandro.
> > ------------------------------
> >
> > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > INFO:root:Wrote R script to
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > through Rscript
> > Seurat loaded, version 5.0.0
> > [1] "Seurat: Reading data"
> > [1] "Seurat: Reading data"
> > [1] "Loading input data matrix"
> > [1] "Loading tsv file with read.delim"
> > [1] "Seurat: Setup"
> > Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes =
> > 200) :
> > argument "counts" is missing, with no default
> > Execution halted
> >
> > real 1m33.191s
> > user 1m17.847s
> > sys 0m1.896s
> > INFO:root:Wrote logfile of R run to
> > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > ERROR:root:R script did not complete successfully. Check
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> analysisLog.txt.
> >
> > —
> > Reply to this email directly, view it on GitHub
> > <#265><<
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Hi….with the 2 mtx.gz files that I tried I did
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
and get that need to specify a dir and not the mtx file for cellranger3-style .mtx
I tried passing the name of a folder w/ the files but didn’t work either.
Can these mtx files be ran by with scanpy?
Thanks,
Alejandro.
--------------------------
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
INFO:root:Matrix input file: bates_matrix.mtx.gz
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 18:52:21.201824
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat 11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 18:52
INFO:root:Loading Scanpy libraries
ERROR:root:For cellranger3-style .mtx files, please specify the directory, not the .mtx.gz file name
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 12:03 PM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Yes try cbScanpy ! It does exactly that !
On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
Hi…Thanks again for your response. I’m trying to setup a somehow generic
process where I take a set of matrix.mtx, features.tsv and barcodes.tsv
files and visualize them w/ the cellbrowser.
I’m not sure if that contains the UMAP coords and clustering or of they
always will so that’s why I thought I had to go thru’ Seurat but if not
needed and you can point me to an example on how to go directly to the
cellbrowser I’d really appreciate.
In the meantime I’ll try to see if I can get the cbScanpy to work w/ these
files!
Thanks!
Alejandro.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 6:53 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Wait... why are you running Seurat? you're running cbSeurat, Sorry I
didn't see that, I was convinced that you're using cbImportSeurat.
I haven't tested cbSeurat in a long time! I should probably retire it.
Don't you have umap coordinates etc as tsv files? If so, you can go
directly to cbBuild.
If you need UMAP coords and clustering and cluster markers, and these
things are not already there in the meta or separate tsv files, you can
also use cbScanpy, which at this point has had a ton more testing.
On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> Hi….The problem is that I’m having a lot of errors when trying to
install
> Seurat 3 or 4. I was able to do it before but seem like it’s failing
now.
> Question: Is there a way of going from the matrix.mtx, features.tsv and
> barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
>
> Thanks!
> Alejandro.
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Thursday, November 30, 2023 at 11:59 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Hm yes I don’t think I’ve tested on Seurat. Do you want share your
matrix
> ?
> Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4 ?
>
> On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
>
> > Hi,
> > I’ve been building my cellbrowsers for matrix files for a while now
and
> > was working fine but after some update the pipeline doesn’t seem to be
> > working any more.
> > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > features.tsv.gz to the cellbrowser by first building the
> exprMatrix.tsv.gz
> > using “cbTool mtx2tsv …” and that step seem to work but then next step
> > cbSeurat is failing.
> > Any idea what can be the problem? Is it a problem of using Seurat
5.0.0
> w/
> > latest version of cellbrowser?
> > Thanks!
> > Alejandro.
> > ------------------------------
> >
> > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > INFO:root:Wrote R script to
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > through Rscript
> > Seurat loaded, version 5.0.0
> > [1] "Seurat: Reading data"
> > [1] "Seurat: Reading data"
> > [1] "Loading input data matrix"
> > [1] "Loading tsv file with read.delim"
> > [1] "Seurat: Setup"
> > Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes =
> > 200) :
> > argument "counts" is missing, with no default
> > Execution halted
> >
> > real 1m33.191s
> > user 1m17.847s
> > sys 0m1.896s
> > INFO:root:Wrote logfile of R run to
> > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > ERROR:root:R script did not complete successfully. Check
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> analysisLog.txt.
> >
> > —
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Yes, the error is because your filenames don't follow the usual convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
…On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
Hi….with the 2 mtx.gz files that I tried I did
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
and get that need to specify a dir and not the mtx file for
cellranger3-style .mtx
I tried passing the name of a folder w/ the files but didn’t work either.
Can these mtx files be ran by with scanpy?
Thanks,
Alejandro.
--------------------------
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
scanpyOut -n test1
INFO:root:Matrix input file: bates_matrix.mtx.gz
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 18:52:21.201824
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 18:52
INFO:root:Loading Scanpy libraries
ERROR:root:For cellranger3-style .mtx files, please specify the directory,
not the .mtx.gz file name
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 12:03 PM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes try cbScanpy ! It does exactly that !
On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> Hi…Thanks again for your response. I’m trying to setup a somehow generic
> process where I take a set of matrix.mtx, features.tsv and barcodes.tsv
> files and visualize them w/ the cellbrowser.
> I’m not sure if that contains the UMAP coords and clustering or of they
> always will so that’s why I thought I had to go thru’ Seurat but if not
> needed and you can point me to an example on how to go directly to the
> cellbrowser I’d really appreciate.
>
> In the meantime I’ll try to see if I can get the cbScanpy to work w/
these
> files!
> Thanks!
> Alejandro.
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 6:53 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> didn't see that, I was convinced that you're using cbImportSeurat.
>
> I haven't tested cbSeurat in a long time! I should probably retire it.
>
> Don't you have umap coordinates etc as tsv files? If so, you can go
> directly to cbBuild.
>
> If you need UMAP coords and clustering and cluster markers, and these
> things are not already there in the meta or separate tsv files, you can
> also use cbScanpy, which at this point has had a ton more testing.
>
> On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
>
> > Hi….The problem is that I’m having a lot of errors when trying to
> install
> > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> now.
> > Question: Is there a way of going from the matrix.mtx, features.tsv
and
> > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> >
> > Thanks!
> > Alejandro.
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Thursday, November 30, 2023 at 11:59 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> matrix
> > ?
> > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4
?
> >
> > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> >
> > > Hi,
> > > I’ve been building my cellbrowsers for matrix files for a while now
> and
> > > was working fine but after some update the pipeline doesn’t seem to
be
> > > working any more.
> > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > features.tsv.gz to the cellbrowser by first building the
> > exprMatrix.tsv.gz
> > > using “cbTool mtx2tsv …” and that step seem to work but then next
step
> > > cbSeurat is failing.
> > > Any idea what can be the problem? Is it a problem of using Seurat
> 5.0.0
> > w/
> > > latest version of cellbrowser?
> > > Thanks!
> > > Alejandro.
> > > ------------------------------
> > >
> > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > INFO:root:Wrote R script to
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > INFO:root:running
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > through Rscript
> > > Seurat loaded, version 5.0.0
> > > [1] "Seurat: Reading data"
> > > [1] "Seurat: Reading data"
> > > [1] "Loading input data matrix"
> > > [1] "Loading tsv file with read.delim"
> > > [1] "Seurat: Setup"
> > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes
=
> > > 200) :
> > > argument "counts" is missing, with no default
> > > Execution halted
> > >
> > > real 1m33.191s
> > > user 1m17.847s
> > > sys 0m1.896s
> > > INFO:root:Wrote logfile of R run to
> > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > ERROR:root:R script did not complete successfully. Check
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > analysisLog.txt.
> > >
> > > —
> > > Reply to this email directly, view it on GitHub
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I’m not sure if I follow. Your example online points to a file
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
But what you mean here is that I need to put all 3 files under a folder and use that name convention?
So I put all 3 files in a folder
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l test1/
total 106608
-rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
-rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
-rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
And then tried passing the folder name but I get error like below seems like is looking for the h5ad file?
cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Matrix input file: test1
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 19:31:04.112141
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat 11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 19:31
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 5865, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname, figDir, logFname)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 5407, in cbScanpy
adata = readMatrixAnndata(matrixFname, samplesOnRows=options.samplesOnRows, genome=options.genome)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4803, in readMatrixAnndata
adata = sc.read(matrixFname, cache=False).T
File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line 127, in read
raise ValueError(
ValueError: Reading with filekey 'test1' failed, the inferred filename PosixPath('write/test1.h5ad') does not exist. If you intended to provide a filename, either use a filename ending on one of the available extensions {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad', 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Monday, December 4, 2023 at 11:15 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Yes, the error is because your filenames don't follow the usual convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
Hi….with the 2 mtx.gz files that I tried I did
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
and get that need to specify a dir and not the mtx file for
cellranger3-style .mtx
I tried passing the name of a folder w/ the files but didn’t work either.
Can these mtx files be ran by with scanpy?
Thanks,
Alejandro.
--------------------------
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
scanpyOut -n test1
INFO:root:Matrix input file: bates_matrix.mtx.gz
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 18:52:21.201824
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 18:52
INFO:root:Loading Scanpy libraries
ERROR:root:For cellranger3-style .mtx files, please specify the directory,
not the .mtx.gz file name
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 12:03 PM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes try cbScanpy ! It does exactly that !
On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> Hi…Thanks again for your response. I’m trying to setup a somehow generic
> process where I take a set of matrix.mtx, features.tsv and barcodes.tsv
> files and visualize them w/ the cellbrowser.
> I’m not sure if that contains the UMAP coords and clustering or of they
> always will so that’s why I thought I had to go thru’ Seurat but if not
> needed and you can point me to an example on how to go directly to the
> cellbrowser I’d really appreciate.
>
> In the meantime I’ll try to see if I can get the cbScanpy to work w/
these
> files!
> Thanks!
> Alejandro.
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 6:53 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> didn't see that, I was convinced that you're using cbImportSeurat.
>
> I haven't tested cbSeurat in a long time! I should probably retire it.
>
> Don't you have umap coordinates etc as tsv files? If so, you can go
> directly to cbBuild.
>
> If you need UMAP coords and clustering and cluster markers, and these
> things are not already there in the meta or separate tsv files, you can
> also use cbScanpy, which at this point has had a ton more testing.
>
> On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
>
> > Hi….The problem is that I’m having a lot of errors when trying to
> install
> > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> now.
> > Question: Is there a way of going from the matrix.mtx, features.tsv
and
> > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> >
> > Thanks!
> > Alejandro.
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Thursday, November 30, 2023 at 11:59 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> matrix
> > ?
> > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4
?
> >
> > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> >
> > > Hi,
> > > I’ve been building my cellbrowsers for matrix files for a while now
> and
> > > was working fine but after some update the pipeline doesn’t seem to
be
> > > working any more.
> > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > features.tsv.gz to the cellbrowser by first building the
> > exprMatrix.tsv.gz
> > > using “cbTool mtx2tsv …” and that step seem to work but then next
step
> > > cbSeurat is failing.
> > > Any idea what can be the problem? Is it a problem of using Seurat
> 5.0.0
> > w/
> > > latest version of cellbrowser?
> > > Thanks!
> > > Alejandro.
> > > ------------------------------
> > >
> > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > INFO:root:Wrote R script to
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > INFO:root:running
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > through Rscript
> > > Seurat loaded, version 5.0.0
> > > [1] "Seurat: Reading data"
> > > [1] "Seurat: Reading data"
> > > [1] "Loading input data matrix"
> > > [1] "Loading tsv file with read.delim"
> > > [1] "Seurat: Setup"
> > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes
=
> > > 200) :
> > > argument "counts" is missing, with no default
> > > Execution halted
> > >
> > > real 1m33.191s
> > > user 1m17.847s
> > > sys 0m1.896s
> > > INFO:root:Wrote logfile of R run to
> > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > ERROR:root:R script did not complete successfully. Check
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > analysisLog.txt.
> > >
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Hi….I tried to run it on the example files from Scanpy example given here https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html
wget http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz>
and I cannot get cbScanpy to run on them.
I built the .h5ad file in python using
import numpy as np
import pandas as pd
import scanpy as sc
adata = sc.read_10x_mtx(
'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx` file
var_names='gene_symbols', # use gene symbols for the variable names (variables-axis index)
cache=True) # write a cache file for faster subsequent reading
adata
and then tried to run the
cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o pbmc3kImportScanpy
But that give errors too.
I
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 11:36 AM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser ***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
I’m not sure if I follow. Your example online points to a file
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
But what you mean here is that I need to put all 3 files under a folder and use that name convention?
So I put all 3 files in a folder
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l test1/
total 106608
-rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
-rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
-rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
And then tried passing the folder name but I get error like below seems like is looking for the h5ad file?
cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Matrix input file: test1
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 19:31:04.112141
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat 11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 19:31
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 5865, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname, figDir, logFname)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 5407, in cbScanpy
adata = readMatrixAnndata(matrixFname, samplesOnRows=options.samplesOnRows, genome=options.genome)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4803, in readMatrixAnndata
adata = sc.read(matrixFname, cache=False).T
File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line 127, in read
raise ValueError(
ValueError: Reading with filekey 'test1' failed, the inferred filename PosixPath('write/test1.h5ad') does not exist. If you intended to provide a filename, either use a filename ending on one of the available extensions {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad', 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Monday, December 4, 2023 at 11:15 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Yes, the error is because your filenames don't follow the usual convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
Hi….with the 2 mtx.gz files that I tried I did
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
and get that need to specify a dir and not the mtx file for
cellranger3-style .mtx
I tried passing the name of a folder w/ the files but didn’t work either.
Can these mtx files be ran by with scanpy?
Thanks,
Alejandro.
--------------------------
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
scanpyOut -n test1
INFO:root:Matrix input file: bates_matrix.mtx.gz
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 18:52:21.201824
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 18:52
INFO:root:Loading Scanpy libraries
ERROR:root:For cellranger3-style .mtx files, please specify the directory,
not the .mtx.gz file name
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 12:03 PM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes try cbScanpy ! It does exactly that !
On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> Hi…Thanks again for your response. I’m trying to setup a somehow generic
> process where I take a set of matrix.mtx, features.tsv and barcodes.tsv
> files and visualize them w/ the cellbrowser.
> I’m not sure if that contains the UMAP coords and clustering or of they
> always will so that’s why I thought I had to go thru’ Seurat but if not
> needed and you can point me to an example on how to go directly to the
> cellbrowser I’d really appreciate.
>
> In the meantime I’ll try to see if I can get the cbScanpy to work w/
these
> files!
> Thanks!
> Alejandro.
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 6:53 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> didn't see that, I was convinced that you're using cbImportSeurat.
>
> I haven't tested cbSeurat in a long time! I should probably retire it.
>
> Don't you have umap coordinates etc as tsv files? If so, you can go
> directly to cbBuild.
>
> If you need UMAP coords and clustering and cluster markers, and these
> things are not already there in the meta or separate tsv files, you can
> also use cbScanpy, which at this point has had a ton more testing.
>
> On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
>
> > Hi….The problem is that I’m having a lot of errors when trying to
> install
> > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> now.
> > Question: Is there a way of going from the matrix.mtx, features.tsv
and
> > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> >
> > Thanks!
> > Alejandro.
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Thursday, November 30, 2023 at 11:59 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> matrix
> > ?
> > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4
?
> >
> > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> >
> > > Hi,
> > > I’ve been building my cellbrowsers for matrix files for a while now
> and
> > > was working fine but after some update the pipeline doesn’t seem to
be
> > > working any more.
> > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > features.tsv.gz to the cellbrowser by first building the
> > exprMatrix.tsv.gz
> > > using “cbTool mtx2tsv …” and that step seem to work but then next
step
> > > cbSeurat is failing.
> > > Any idea what can be the problem? Is it a problem of using Seurat
> 5.0.0
> > w/
> > > latest version of cellbrowser?
> > > Thanks!
> > > Alejandro.
> > > ------------------------------
> > >
> > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > INFO:root:Wrote R script to
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > INFO:root:running
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > through Rscript
> > > Seurat loaded, version 5.0.0
> > > [1] "Seurat: Reading data"
> > > [1] "Seurat: Reading data"
> > > [1] "Loading input data matrix"
> > > [1] "Loading tsv file with read.delim"
> > > [1] "Seurat: Setup"
> > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes
=
> > > 200) :
> > > argument "counts" is missing, with no default
> > > Execution halted
> > >
> > > real 1m33.191s
> > > user 1m17.847s
> > > sys 0m1.896s
> > > INFO:root:Wrote logfile of R run to
> > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > ERROR:root:R script did not complete successfully. Check
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > analysisLog.txt.
> > >
> > > —
> > > Reply to this email directly, view it on GitHub
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I actually uninstall cellbrowser and installed it again and now is doing a bit more but still throwing errors:
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data] cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
INFO:root:Loading Scanpy libraries
INFO:root:Creating scanpyOut
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-05 04:30:26.199478
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.2.3
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat 11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-05 04:30
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
INFO:root:Data has 2700 samples/observations
INFO:root:Data has 32738 genes/variables
INFO:root:Basic filtering: keep only cells with min 200 genes
INFO:root:Basic filtering: keep only gene with min 3 cells
INFO:root:After filtering: Data has 2700 samples/observations and 13714 genes/variables
INFO:root:Making gene names unique
INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
INFO:root:Auto-detected gene IDs type: symbols
INFO:root:Remove cells with more than 0.050000 percent of mitochondrial genes
INFO:root:Computing percentage of mitochondrial genes
WARNING: saving figure to file scanpyOut/figs/violin.png
INFO:root:Remove cells with less than 10 and more than 15000 genes
INFO:root:Keeping only cells with < 15000 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714 genes/variables
INFO:root:Keeping only cells with > 10 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714 genes/variables
INFO:root:Expression normalization, counts per cell = 10000
INFO:root:Did log2'ing of data
INFO:root:Finding highly variable genes
WARNING: saving figure to file scanpyOut/figs/filter_genes_dispersion.png
INFO:root:After high-var filtering: Data has 2643 samples/observations and 1844 genes/variables
INFO:root:Regressing out percent_mito and number of UMIs
INFO:root:Scaling data, max_value=10
INFO:root:Performing initial PCA, number of PCs: 100
WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
INFO:root:Estimating number of useful PCs based on Shekar et al, Cell 2016
INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8, STAR methods
INFO:root:7 PCs will be used for tSNE and clustering
INFO:root:Performing tSNE
INFO:root:Running knn, using 7 PCs and 6 neighbors
INFO:root:Performing Louvain Clustering, resolution 1.000000
INFO:root:Found 13 louvain clusters
INFO:root:Using cluster annotation from field: louvain
WARNING: saving figure to file scanpyOut/figs/tsne.png
INFO:root:Performing UMAP
INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
INFO:root:Finding top markers for each cluster
INFO:root:Loading Scanpy libraries
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 6643, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname, figDir, logFname, skipMarkers)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 6432, in cbScanpy
adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4651, in runSafeRankGenesGroups
clusterCellCounts = list(adata.obs.groupby([clusterField]).apply(len).iteritems())
File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py", line 6204, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'iteritems'
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 7:49 PM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser ***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Hi….I tried to run it on the example files from Scanpy example given here https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html
wget http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz>
and I cannot get cbScanpy to run on them.
I built the .h5ad file in python using
import numpy as np
import pandas as pd
import scanpy as sc
adata = sc.read_10x_mtx(
'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx` file
var_names='gene_symbols', # use gene symbols for the variable names (variables-axis index)
cache=True) # write a cache file for faster subsequent reading
adata
and then tried to run the
cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o pbmc3kImportScanpy
But that give errors too.
I
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 11:36 AM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser ***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
I’m not sure if I follow. Your example online points to a file
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
But what you mean here is that I need to put all 3 files under a folder and use that name convention?
So I put all 3 files in a folder
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l test1/
total 106608
-rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
-rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
-rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
And then tried passing the folder name but I get error like below seems like is looking for the h5ad file?
cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Matrix input file: test1
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 19:31:04.112141
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat 11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 19:31
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 5865, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname, figDir, logFname)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 5407, in cbScanpy
adata = readMatrixAnndata(matrixFname, samplesOnRows=options.samplesOnRows, genome=options.genome)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4803, in readMatrixAnndata
adata = sc.read(matrixFname, cache=False).T
File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line 127, in read
raise ValueError(
ValueError: Reading with filekey 'test1' failed, the inferred filename PosixPath('write/test1.h5ad') does not exist. If you intended to provide a filename, either use a filename ending on one of the available extensions {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad', 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Monday, December 4, 2023 at 11:15 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Yes, the error is because your filenames don't follow the usual convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
Hi….with the 2 mtx.gz files that I tried I did
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
and get that need to specify a dir and not the mtx file for
cellranger3-style .mtx
I tried passing the name of a folder w/ the files but didn’t work either.
Can these mtx files be ran by with scanpy?
Thanks,
Alejandro.
--------------------------
cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
scanpyOut -n test1
INFO:root:Matrix input file: bates_matrix.mtx.gz
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 18:52:21.201824
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 18:52
INFO:root:Loading Scanpy libraries
ERROR:root:For cellranger3-style .mtx files, please specify the directory,
not the .mtx.gz file name
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Friday, December 1, 2023 at 12:03 PM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes try cbScanpy ! It does exactly that !
On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> Hi…Thanks again for your response. I’m trying to setup a somehow generic
> process where I take a set of matrix.mtx, features.tsv and barcodes.tsv
> files and visualize them w/ the cellbrowser.
> I’m not sure if that contains the UMAP coords and clustering or of they
> always will so that’s why I thought I had to go thru’ Seurat but if not
> needed and you can point me to an example on how to go directly to the
> cellbrowser I’d really appreciate.
>
> In the meantime I’ll try to see if I can get the cbScanpy to work w/
these
> files!
> Thanks!
> Alejandro.
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 6:53 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> didn't see that, I was convinced that you're using cbImportSeurat.
>
> I haven't tested cbSeurat in a long time! I should probably retire it.
>
> Don't you have umap coordinates etc as tsv files? If so, you can go
> directly to cbBuild.
>
> If you need UMAP coords and clustering and cluster markers, and these
> things are not already there in the meta or separate tsv files, you can
> also use cbScanpy, which at this point has had a ton more testing.
>
> On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
>
> > Hi….The problem is that I’m having a lot of errors when trying to
> install
> > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> now.
> > Question: Is there a way of going from the matrix.mtx, features.tsv
and
> > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> >
> > Thanks!
> > Alejandro.
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Thursday, November 30, 2023 at 11:59 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> matrix
> > ?
> > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or 4
?
> >
> > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> >
> > > Hi,
> > > I’ve been building my cellbrowsers for matrix files for a while now
> and
> > > was working fine but after some update the pipeline doesn’t seem to
be
> > > working any more.
> > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > features.tsv.gz to the cellbrowser by first building the
> > exprMatrix.tsv.gz
> > > using “cbTool mtx2tsv …” and that step seem to work but then next
step
> > > cbSeurat is failing.
> > > Any idea what can be the problem? Is it a problem of using Seurat
> 5.0.0
> > w/
> > > latest version of cellbrowser?
> > > Thanks!
> > > Alejandro.
> > > ------------------------------
> > >
> > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > INFO:root:Wrote R script to
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > INFO:root:running
/var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > through Rscript
> > > Seurat loaded, version 5.0.0
> > > [1] "Seurat: Reading data"
> > > [1] "Seurat: Reading data"
> > > [1] "Loading input data matrix"
> > > [1] "Loading tsv file with read.delim"
> > > [1] "Seurat: Setup"
> > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes
=
> > > 200) :
> > > argument "counts" is missing, with no default
> > > Execution halted
> > >
> > > real 1m33.191s
> > > user 1m17.847s
> > > sys 0m1.896s
> > > INFO:root:Wrote logfile of R run to
> > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > ERROR:root:R script did not complete successfully. Check
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > analysisLog.txt.
> > >
> > > —
> > > Reply to this email directly, view it on GitHub
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Great, so this almost worked, it's only stuck at the markers calculation
step at the end now. This should be easy to fix.
You're using Python 3.9 from 2020 and combine that with the most recent
scanpy version, just a few weeks old. We didn't test this combination. You
could downgrade scanpy to a few versions older. But yes, it should normally
work, it's possible I have to add yet another workaround (I've kept adding
workarounds for the different scanpy versions, every few months, something
is breaking there).
As soon as I can reproduce this error, I can fix it. Can you tell me where
you downloaded the mtx file from? Is this your own file or a 10X pbmc demo
file?
…On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
I actually uninstall cellbrowser and installed it again and now is doing a
bit more but still throwing errors:
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
pbmc3k
INFO:root:Loading Scanpy libraries
INFO:root:Creating scanpyOut
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e
filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-05 04:30:26.199478
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.2.3
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-05 04:30
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
INFO:root:Data has 2700 samples/observations
INFO:root:Data has 32738 genes/variables
INFO:root:Basic filtering: keep only cells with min 200 genes
INFO:root:Basic filtering: keep only gene with min 3 cells
INFO:root:After filtering: Data has 2700 samples/observations and 13714
genes/variables
INFO:root:Making gene names unique
INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
INFO:root:Auto-detected gene IDs type: symbols
INFO:root:Remove cells with more than 0.050000 percent of mitochondrial
genes
INFO:root:Computing percentage of mitochondrial genes
WARNING: saving figure to file scanpyOut/figs/violin.png
INFO:root:Remove cells with less than 10 and more than 15000 genes
INFO:root:Keeping only cells with < 15000 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714
genes/variables
INFO:root:Keeping only cells with > 10 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714
genes/variables
INFO:root:Expression normalization, counts per cell = 10000
INFO:root:Did log2'ing of data
INFO:root:Finding highly variable genes
WARNING: saving figure to file scanpyOut/figs/filter_genes_dispersion.png
INFO:root:After high-var filtering: Data has 2643 samples/observations and
1844 genes/variables
INFO:root:Regressing out percent_mito and number of UMIs
INFO:root:Scaling data, max_value=10
INFO:root:Performing initial PCA, number of PCs: 100
WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
INFO:root:Estimating number of useful PCs based on Shekar et al, Cell 2016
INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8,
STAR methods
INFO:root:7 PCs will be used for tSNE and clustering
INFO:root:Performing tSNE
INFO:root:Running knn, using 7 PCs and 6 neighbors
INFO:root:Performing Louvain Clustering, resolution 1.000000
INFO:root:Found 13 louvain clusters
INFO:root:Using cluster annotation from field: louvain
WARNING: saving figure to file scanpyOut/figs/tsne.png
INFO:root:Performing UMAP
INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
INFO:root:Finding top markers for each cluster
INFO:root:Loading Scanpy libraries
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6643, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname, skipMarkers)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6432, in cbScanpy
adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4651, in runSafeRankGenesGroups
clusterCellCounts =
list(adata.obs.groupby([clusterField]).apply(len).iteritems())
File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
line 6204, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'iteritems'
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 7:49 PM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Hi….I tried to run it on the example files from Scanpy example given here
https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html
wget
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz
-O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz>
and I cannot get cbScanpy to run on them.
I built the .h5ad file in python using
import numpy as np
import pandas as pd
import scanpy as sc
adata = sc.read_10x_mtx(
'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx`
file
var_names='gene_symbols', # use gene symbols for the variable names
(variables-axis index)
cache=True) # write a cache file for faster subsequent reading
adata
and then tried to run the
cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
pbmc3kImportScanpy
But that give errors too.
I
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 11:36 AM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
I’m not sure if I follow. Your example online points to a file
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
pbmc3k
But what you mean here is that I need to put all 3 files under a folder
and use that name convention?
So I put all 3 files in a folder
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
test1/
total 106608
-rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
-rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
-rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
And then tried passing the folder name but I get error like below seems
like is looking for the h5ad file?
cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
testOut
INFO:root:Matrix input file: test1
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 19:31:04.112141
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 19:31
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 5865, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 5407, in cbScanpy
adata = readMatrixAnndata(matrixFname,
samplesOnRows=options.samplesOnRows, genome=options.genome)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4803, in readMatrixAnndata
adata = sc.read(matrixFname, cache=False).T
File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line
127, in read
raise ValueError(
ValueError: Reading with filekey 'test1' failed, the inferred filename
PosixPath('write/test1.h5ad') does not exist. If you intended to provide a
filename, either use a filename ending on one of the available extensions
{'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad',
'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Monday, December 4, 2023 at 11:15 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes, the error is because your filenames don't follow the usual
convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
> Hi….with the 2 mtx.gz files that I tried I did
>
>
>
> cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
>
>
>
> and get that need to specify a dir and not the mtx file for
> cellranger3-style .mtx
>
> I tried passing the name of a folder w/ the files but didn’t work
either.
>
> Can these mtx files be ran by with scanpy?
>
> Thanks,
>
> Alejandro.
>
> --------------------------
>
>
>
> cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:cbScanpy $Id$
>
> INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> scanpyOut -n test1
>
> INFO:root:Matrix input file: bates_matrix.mtx.gz
>
> INFO:root:Restricting OPENBLAS to 4 threads
>
> INFO:root:Start time: 2023-12-04 18:52:21.201824
>
> -----
>
> anndata 0.10.3
>
> scanpy 1.9.6
>
> -----
>
> PIL 10.0.0
>
> asciitree NA
>
> cellbrowser v1.0.1
>
> cffi 1.14.5
>
> colorama 0.4.4
>
> cycler 0.12.1
>
> cython_runtime NA
>
> dateutil 2.8.2
>
> entrypoints 0.4
>
> exceptiongroup 1.2.0
>
> fasteners 0.18
>
> get_annotations NA
>
> h5py 3.10.0
>
> igraph 0.10.8
>
> importlib_resources NA
>
> joblib 1.3.2
>
> kiwisolver 1.4.5
>
> llvmlite 0.41.1
>
> louvain 0.8.1
>
> matplotlib 3.8.2
>
> mpl_toolkits NA
>
> natsort 8.4.0
>
> numba 0.58.1
>
> numcodecs 0.11.0
>
> numpy 1.25.2
>
> packaging 23.1
>
> pandas 2.1.3
>
> pkg_resources NA
>
> psutil 5.8.0
>
> pyparsing 3.1.1
>
> pytz 2021.1
>
> scipy 1.11.3
>
> session_info 1.0.0
>
> setuptools_scm NA
>
> six 1.15.0
>
> sklearn 1.3.2
>
> texttable 1.7.0
>
> threadpoolctl 3.2.0
>
> typing_extensions NA
>
> yaml 5.4.1
>
> zarr 2.16.1
>
> zipp NA
>
> zoneinfo NA
>
> -----
>
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
>
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
>
> -----
>
> Session information updated at 2023-12-04 18:52
>
> INFO:root:Loading Scanpy libraries
>
> ERROR:root:For cellranger3-style .mtx files, please specify the
directory,
> not the .mtx.gz file name
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 12:03 PM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Yes try cbScanpy ! It does exactly that !
>
> On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
>
> > Hi…Thanks again for your response. I’m trying to setup a somehow
generic
> > process where I take a set of matrix.mtx, features.tsv and
barcodes.tsv
> > files and visualize them w/ the cellbrowser.
> > I’m not sure if that contains the UMAP coords and clustering or of
they
> > always will so that’s why I thought I had to go thru’ Seurat but if
not
> > needed and you can point me to an example on how to go directly to the
> > cellbrowser I’d really appreciate.
> >
> > In the meantime I’ll try to see if I can get the cbScanpy to work w/
> these
> > files!
> > Thanks!
> > Alejandro.
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Friday, December 1, 2023 at 6:53 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> > didn't see that, I was convinced that you're using cbImportSeurat.
> >
> > I haven't tested cbSeurat in a long time! I should probably retire it.
> >
> > Don't you have umap coordinates etc as tsv files? If so, you can go
> > directly to cbBuild.
> >
> > If you need UMAP coords and clustering and cluster markers, and these
> > things are not already there in the meta or separate tsv files, you
can
> > also use cbScanpy, which at this point has had a ton more testing.
> >
> > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> >
> > > Hi….The problem is that I’m having a lot of errors when trying to
> > install
> > > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> > now.
> > > Question: Is there a way of going from the matrix.mtx, features.tsv
> and
> > > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> > >
> > > Thanks!
> > > Alejandro.
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> > matrix
> > > ?
> > > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or
4
> ?
> > >
> > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > >
> > > > Hi,
> > > > I’ve been building my cellbrowsers for matrix files for a while
now
> > and
> > > > was working fine but after some update the pipeline doesn’t seem
to
> be
> > > > working any more.
> > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > features.tsv.gz to the cellbrowser by first building the
> > > exprMatrix.tsv.gz
> > > > using “cbTool mtx2tsv …” and that step seem to work but then next
> step
> > > > cbSeurat is failing.
> > > > Any idea what can be the problem? Is it a problem of using Seurat
> > 5.0.0
> > > w/
> > > > latest version of cellbrowser?
> > > > Thanks!
> > > > Alejandro.
> > > > ------------------------------
> > > >
> > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > INFO:root:Wrote R script to
> > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > INFO:root:running
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > through Rscript
> > > > Seurat loaded, version 5.0.0
> > > > [1] "Seurat: Reading data"
> > > > [1] "Seurat: Reading data"
> > > > [1] "Loading input data matrix"
> > > > [1] "Loading tsv file with read.delim"
> > > > [1] "Seurat: Setup"
> > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
min.genes
> =
> > > > 200) :
> > > > argument "counts" is missing, with no default
> > > > Execution halted
> > > >
> > > > real 1m33.191s
> > > > user 1m17.847s
> > > > sys 0m1.896s
> > > > INFO:root:Wrote logfile of R run to
> > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > ERROR:root:R script did not complete successfully. Check
> > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > analysisLog.txt.
> > > >
> > > > —
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It’t the pbmc demo file from the scanpy tutorial
Thanks!!!
Alejandro.
Sent from my iPhone
On Dec 5, 2023, at 1:15 AM, Maximilian Haeussler ***@***.***> wrote:
Great, so this almost worked, it's only stuck at the markers calculation
step at the end now. This should be easy to fix.
You're using Python 3.9 from 2020 and combine that with the most recent
scanpy version, just a few weeks old. We didn't test this combination. You
could downgrade scanpy to a few versions older. But yes, it should normally
work, it's possible I have to add yet another workaround (I've kept adding
workarounds for the different scanpy versions, every few months, something
is breaking there).
As soon as I can reproduce this error, I can fix it. Can you tell me where
you downloaded the mtx file from? Is this your own file or a 10X pbmc demo
file?
On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
I actually uninstall cellbrowser and installed it again and now is doing a
bit more but still throwing errors:
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
pbmc3k
INFO:root:Loading Scanpy libraries
INFO:root:Creating scanpyOut
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e
filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-05 04:30:26.199478
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.2.3
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-05 04:30
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
INFO:root:Data has 2700 samples/observations
INFO:root:Data has 32738 genes/variables
INFO:root:Basic filtering: keep only cells with min 200 genes
INFO:root:Basic filtering: keep only gene with min 3 cells
INFO:root:After filtering: Data has 2700 samples/observations and 13714
genes/variables
INFO:root:Making gene names unique
INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
INFO:root:Auto-detected gene IDs type: symbols
INFO:root:Remove cells with more than 0.050000 percent of mitochondrial
genes
INFO:root:Computing percentage of mitochondrial genes
WARNING: saving figure to file scanpyOut/figs/violin.png
INFO:root:Remove cells with less than 10 and more than 15000 genes
INFO:root:Keeping only cells with < 15000 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714
genes/variables
INFO:root:Keeping only cells with > 10 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714
genes/variables
INFO:root:Expression normalization, counts per cell = 10000
INFO:root:Did log2'ing of data
INFO:root:Finding highly variable genes
WARNING: saving figure to file scanpyOut/figs/filter_genes_dispersion.png
INFO:root:After high-var filtering: Data has 2643 samples/observations and
1844 genes/variables
INFO:root:Regressing out percent_mito and number of UMIs
INFO:root:Scaling data, max_value=10
INFO:root:Performing initial PCA, number of PCs: 100
WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
INFO:root:Estimating number of useful PCs based on Shekar et al, Cell 2016
INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8<https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=LRCerhXenZ3f2SWEPhr8kULBEGklU2NYVJ-O5nUQ-tA&e=>,
STAR methods
INFO:root:7 PCs will be used for tSNE and clustering
INFO:root:Performing tSNE
INFO:root:Running knn, using 7 PCs and 6 neighbors
INFO:root:Performing Louvain Clustering, resolution 1.000000
INFO:root:Found 13 louvain clusters
INFO:root:Using cluster annotation from field: louvain
WARNING: saving figure to file scanpyOut/figs/tsne.png
INFO:root:Performing UMAP
INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
INFO:root:Finding top markers for each cluster
INFO:root:Loading Scanpy libraries
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6643, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname, skipMarkers)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6432, in cbScanpy
adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4651, in runSafeRankGenesGroups
clusterCellCounts =
list(adata.obs.groupby([clusterField]).apply(len).iteritems())
File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
line 6204, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'iteritems'
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 7:49 PM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Hi….I tried to run it on the example files from Scanpy example given here
https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html<https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=fwTJ3jAfqNQubzg5eA4igcNVVQaoKw84DwvDYjI16tM&e=>
wget
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=>
-O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz><https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=>
and I cannot get cbScanpy to run on them.
I built the .h5ad file in python using
import numpy as np
import pandas as pd
import scanpy as sc
adata = sc.read_10x_mtx(
'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx`
file
var_names='gene_symbols', # use gene symbols for the variable names
(variables-axis index)
cache=True) # write a cache file for faster subsequent reading
adata
and then tried to run the
cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
pbmc3kImportScanpy
But that give errors too.
I
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 11:36 AM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
I’m not sure if I follow. Your example online points to a file
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
pbmc3k
But what you mean here is that I need to put all 3 files under a folder
and use that name convention?
So I put all 3 files in a folder
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
test1/
total 106608
-rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
-rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
-rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
And then tried passing the folder name but I get error like below seems
like is looking for the h5ad file?
cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
testOut
INFO:root:Matrix input file: test1
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 19:31:04.112141
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 19:31
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 5865, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 5407, in cbScanpy
adata = readMatrixAnndata(matrixFname,
samplesOnRows=options.samplesOnRows, genome=options.genome)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4803, in readMatrixAnndata
adata = sc.read(matrixFname, cache=False).T
File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line
127, in read
raise ValueError(
ValueError: Reading with filekey 'test1' failed, the inferred filename
PosixPath('write/test1.h5ad') does not exist. If you intended to provide a
filename, either use a filename ending on one of the available extensions
{'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad',
'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Monday, December 4, 2023 at 11:15 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes, the error is because your filenames don't follow the usual
convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
> Hi….with the 2 mtx.gz files that I tried I did
>
>
>
> cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
>
>
>
> and get that need to specify a dir and not the mtx file for
> cellranger3-style .mtx
>
> I tried passing the name of a folder w/ the files but didn’t work
either.
>
> Can these mtx files be ran by with scanpy?
>
> Thanks,
>
> Alejandro.
>
> --------------------------
>
>
>
> cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:cbScanpy $Id$
>
> INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> scanpyOut -n test1
>
> INFO:root:Matrix input file: bates_matrix.mtx.gz
>
> INFO:root:Restricting OPENBLAS to 4 threads
>
> INFO:root:Start time: 2023-12-04 18:52:21.201824
>
> -----
>
> anndata 0.10.3
>
> scanpy 1.9.6
>
> -----
>
> PIL 10.0.0
>
> asciitree NA
>
> cellbrowser v1.0.1
>
> cffi 1.14.5
>
> colorama 0.4.4
>
> cycler 0.12.1
>
> cython_runtime NA
>
> dateutil 2.8.2
>
> entrypoints 0.4
>
> exceptiongroup 1.2.0
>
> fasteners 0.18
>
> get_annotations NA
>
> h5py 3.10.0
>
> igraph 0.10.8
>
> importlib_resources NA
>
> joblib 1.3.2
>
> kiwisolver 1.4.5
>
> llvmlite 0.41.1
>
> louvain 0.8.1
>
> matplotlib 3.8.2
>
> mpl_toolkits NA
>
> natsort 8.4.0
>
> numba 0.58.1
>
> numcodecs 0.11.0
>
> numpy 1.25.2
>
> packaging 23.1
>
> pandas 2.1.3
>
> pkg_resources NA
>
> psutil 5.8.0
>
> pyparsing 3.1.1
>
> pytz 2021.1
>
> scipy 1.11.3
>
> session_info 1.0.0
>
> setuptools_scm NA
>
> six 1.15.0
>
> sklearn 1.3.2
>
> texttable 1.7.0
>
> threadpoolctl 3.2.0
>
> typing_extensions NA
>
> yaml 5.4.1
>
> zarr 2.16.1
>
> zipp NA
>
> zoneinfo NA
>
> -----
>
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
>
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
>
> -----
>
> Session information updated at 2023-12-04 18:52
>
> INFO:root:Loading Scanpy libraries
>
> ERROR:root:For cellranger3-style .mtx files, please specify the
directory,
> not the .mtx.gz file name
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 12:03 PM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Yes try cbScanpy ! It does exactly that !
>
> On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
>
> > Hi…Thanks again for your response. I’m trying to setup a somehow
generic
> > process where I take a set of matrix.mtx, features.tsv and
barcodes.tsv
> > files and visualize them w/ the cellbrowser.
> > I’m not sure if that contains the UMAP coords and clustering or of
they
> > always will so that’s why I thought I had to go thru’ Seurat but if
not
> > needed and you can point me to an example on how to go directly to the
> > cellbrowser I’d really appreciate.
> >
> > In the meantime I’ll try to see if I can get the cbScanpy to work w/
> these
> > files!
> > Thanks!
> > Alejandro.
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Friday, December 1, 2023 at 6:53 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> > didn't see that, I was convinced that you're using cbImportSeurat.
> >
> > I haven't tested cbSeurat in a long time! I should probably retire it.
> >
> > Don't you have umap coordinates etc as tsv files? If so, you can go
> > directly to cbBuild.
> >
> > If you need UMAP coords and clustering and cluster markers, and these
> > things are not already there in the meta or separate tsv files, you
can
> > also use cbScanpy, which at this point has had a ton more testing.
> >
> > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> >
> > > Hi….The problem is that I’m having a lot of errors when trying to
> > install
> > > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> > now.
> > > Question: Is there a way of going from the matrix.mtx, features.tsv
> and
> > > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> > >
> > > Thanks!
> > > Alejandro.
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> > matrix
> > > ?
> > > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or
4
> ?
> > >
> > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > >
> > > > Hi,
> > > > I’ve been building my cellbrowsers for matrix files for a while
now
> > and
> > > > was working fine but after some update the pipeline doesn’t seem
to
> be
> > > > working any more.
> > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > features.tsv.gz to the cellbrowser by first building the
> > > exprMatrix.tsv.gz
> > > > using “cbTool mtx2tsv …” and that step seem to work but then next
> step
> > > > cbSeurat is failing.
> > > > Any idea what can be the problem? Is it a problem of using Seurat
> > 5.0.0
> > > w/
> > > > latest version of cellbrowser?
> > > > Thanks!
> > > > Alejandro.
> > > > ------------------------------
> > > >
> > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > INFO:root:Wrote R script to
> > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > INFO:root:running
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > through Rscript
> > > > Seurat loaded, version 5.0.0
> > > > [1] "Seurat: Reading data"
> > > > [1] "Seurat: Reading data"
> > > > [1] "Loading input data matrix"
> > > > [1] "Loading tsv file with read.delim"
> > > > [1] "Seurat: Setup"
> > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
min.genes
> =
> > > > 200) :
> > > > argument "counts" is missing, with no default
> > > > Execution halted
> > > >
> > > > real 1m33.191s
> > > > user 1m17.847s
> > > > sys 0m1.896s
> > > > INFO:root:Wrote logfile of R run to
> > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > ERROR:root:R script did not complete successfully. Check
> > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > analysisLog.txt.
> > > >
> > > > —
> > > > Reply to this email directly, view it on GitHub
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wget
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=>
-O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz><https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=>
Sent from my iPhone
On Dec 5, 2023, at 1:15 AM, Maximilian Haeussler ***@***.***> wrote:
Great, so this almost worked, it's only stuck at the markers calculation
step at the end now. This should be easy to fix.
You're using Python 3.9 from 2020 and combine that with the most recent
scanpy version, just a few weeks old. We didn't test this combination. You
could downgrade scanpy to a few versions older. But yes, it should normally
work, it's possible I have to add yet another workaround (I've kept adding
workarounds for the different scanpy versions, every few months, something
is breaking there).
As soon as I can reproduce this error, I can fix it. Can you tell me where
you downloaded the mtx file from? Is this your own file or a 10X pbmc demo
file?
On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
I actually uninstall cellbrowser and installed it again and now is doing a
bit more but still throwing errors:
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
pbmc3k
INFO:root:Loading Scanpy libraries
INFO:root:Creating scanpyOut
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e
filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-05 04:30:26.199478
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.2.3
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-05 04:30
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
INFO:root:Data has 2700 samples/observations
INFO:root:Data has 32738 genes/variables
INFO:root:Basic filtering: keep only cells with min 200 genes
INFO:root:Basic filtering: keep only gene with min 3 cells
INFO:root:After filtering: Data has 2700 samples/observations and 13714
genes/variables
INFO:root:Making gene names unique
INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
INFO:root:Auto-detected gene IDs type: symbols
INFO:root:Remove cells with more than 0.050000 percent of mitochondrial
genes
INFO:root:Computing percentage of mitochondrial genes
WARNING: saving figure to file scanpyOut/figs/violin.png
INFO:root:Remove cells with less than 10 and more than 15000 genes
INFO:root:Keeping only cells with < 15000 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714
genes/variables
INFO:root:Keeping only cells with > 10 genes
INFO:root:After filtering: Data has 2643 samples/observations and 13714
genes/variables
INFO:root:Expression normalization, counts per cell = 10000
INFO:root:Did log2'ing of data
INFO:root:Finding highly variable genes
WARNING: saving figure to file scanpyOut/figs/filter_genes_dispersion.png
INFO:root:After high-var filtering: Data has 2643 samples/observations and
1844 genes/variables
INFO:root:Regressing out percent_mito and number of UMIs
INFO:root:Scaling data, max_value=10
INFO:root:Performing initial PCA, number of PCs: 100
WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
INFO:root:Estimating number of useful PCs based on Shekar et al, Cell 2016
INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8<https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=LRCerhXenZ3f2SWEPhr8kULBEGklU2NYVJ-O5nUQ-tA&e=>,
STAR methods
INFO:root:7 PCs will be used for tSNE and clustering
INFO:root:Performing tSNE
INFO:root:Running knn, using 7 PCs and 6 neighbors
INFO:root:Performing Louvain Clustering, resolution 1.000000
INFO:root:Found 13 louvain clusters
INFO:root:Using cluster annotation from field: louvain
WARNING: saving figure to file scanpyOut/figs/tsne.png
INFO:root:Performing UMAP
INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
INFO:root:Finding top markers for each cluster
INFO:root:Loading Scanpy libraries
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6643, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname, skipMarkers)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6432, in cbScanpy
adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4651, in runSafeRankGenesGroups
clusterCellCounts =
list(adata.obs.groupby([clusterField]).apply(len).iteritems())
File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
line 6204, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'iteritems'
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 7:49 PM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Hi….I tried to run it on the example files from Scanpy example given here
https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html<https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=fwTJ3jAfqNQubzg5eA4igcNVVQaoKw84DwvDYjI16tM&e=>
wget
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=>
-O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz><https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=>
and I cannot get cbScanpy to run on them.
I built the .h5ad file in python using
import numpy as np
import pandas as pd
import scanpy as sc
adata = sc.read_10x_mtx(
'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx`
file
var_names='gene_symbols', # use gene symbols for the variable names
(variables-axis index)
cache=True) # write a cache file for faster subsequent reading
adata
and then tried to run the
cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
pbmc3kImportScanpy
But that give errors too.
I
From: Alejandro Bugacov ***@***.***>
Date: Monday, December 4, 2023 at 11:36 AM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
I’m not sure if I follow. Your example online points to a file
cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
pbmc3k
But what you mean here is that I need to put all 3 files under a folder
and use that name convention?
So I put all 3 files in a folder
facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
test1/
total 106608
-rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
-rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
-rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
And then tried passing the folder name but I get error like below seems
like is looking for the h5ad file?
cbScanpy -e test1 -o scanpyOut -n testOut
INFO:root:Loading Scanpy libraries
INFO:root:Loading Scanpy libraries
INFO:root:cbScanpy $Id$
INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
testOut
INFO:root:Matrix input file: test1
INFO:root:Restricting OPENBLAS to 4 threads
INFO:root:Start time: 2023-12-04 19:31:04.112141
-----
anndata 0.10.3
scanpy 1.9.6
-----
PIL 10.0.0
asciitree NA
cellbrowser v1.0.1
cffi 1.14.5
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
entrypoints 0.4
exceptiongroup 1.2.0
fasteners 0.18
get_annotations NA
h5py 3.10.0
igraph 0.10.8
importlib_resources NA
joblib 1.3.2
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.8.2
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numcodecs 0.11.0
numpy 1.25.2
packaging 23.1
pandas 2.1.3
pkg_resources NA
psutil 5.8.0
pyparsing 3.1.1
pytz 2021.1
scipy 1.11.3
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 1.3.2
texttable 1.7.0
threadpoolctl 3.2.0
typing_extensions NA
yaml 5.4.1
zarr 2.16.1
zipp NA
zoneinfo NA
-----
Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
11.4.1-2)]
Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
-----
Session information updated at 2023-12-04 19:31
INFO:root:Loading Scanpy libraries
INFO:root:Loading expression matrix: mtx format
Traceback (most recent call last):
File "/usr/local/bin/cbScanpy", line 8, in <module>
sys.exit(cbScanpyCli())
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 5865, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 5407, in cbScanpy
adata = readMatrixAnndata(matrixFname,
samplesOnRows=options.samplesOnRows, genome=options.genome)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4803, in readMatrixAnndata
adata = sc.read(matrixFname, cache=False).T
File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line
127, in read
raise ValueError(
ValueError: Reading with filekey 'test1' failed, the inferred filename
PosixPath('write/test1.h5ad') does not exist. If you intended to provide a
filename, either use a filename ending on one of the available extensions
{'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad',
'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Monday, December 4, 2023 at 11:15 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Yes, the error is because your filenames don't follow the usual
convention.
Can you rename your files to matrix.mtx.gz and features.tsv.gz and
barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
again.
I am not sure how/if I can solve this, this is a problem in scanpy, as it
only accepts the directory name, I think.
On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
> Hi….with the 2 mtx.gz files that I tried I did
>
>
>
> cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
>
>
>
> and get that need to specify a dir and not the mtx file for
> cellranger3-style .mtx
>
> I tried passing the name of a folder w/ the files but didn’t work
either.
>
> Can these mtx files be ran by with scanpy?
>
> Thanks,
>
> Alejandro.
>
> --------------------------
>
>
>
> cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:cbScanpy $Id$
>
> INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> scanpyOut -n test1
>
> INFO:root:Matrix input file: bates_matrix.mtx.gz
>
> INFO:root:Restricting OPENBLAS to 4 threads
>
> INFO:root:Start time: 2023-12-04 18:52:21.201824
>
> -----
>
> anndata 0.10.3
>
> scanpy 1.9.6
>
> -----
>
> PIL 10.0.0
>
> asciitree NA
>
> cellbrowser v1.0.1
>
> cffi 1.14.5
>
> colorama 0.4.4
>
> cycler 0.12.1
>
> cython_runtime NA
>
> dateutil 2.8.2
>
> entrypoints 0.4
>
> exceptiongroup 1.2.0
>
> fasteners 0.18
>
> get_annotations NA
>
> h5py 3.10.0
>
> igraph 0.10.8
>
> importlib_resources NA
>
> joblib 1.3.2
>
> kiwisolver 1.4.5
>
> llvmlite 0.41.1
>
> louvain 0.8.1
>
> matplotlib 3.8.2
>
> mpl_toolkits NA
>
> natsort 8.4.0
>
> numba 0.58.1
>
> numcodecs 0.11.0
>
> numpy 1.25.2
>
> packaging 23.1
>
> pandas 2.1.3
>
> pkg_resources NA
>
> psutil 5.8.0
>
> pyparsing 3.1.1
>
> pytz 2021.1
>
> scipy 1.11.3
>
> session_info 1.0.0
>
> setuptools_scm NA
>
> six 1.15.0
>
> sklearn 1.3.2
>
> texttable 1.7.0
>
> threadpoolctl 3.2.0
>
> typing_extensions NA
>
> yaml 5.4.1
>
> zarr 2.16.1
>
> zipp NA
>
> zoneinfo NA
>
> -----
>
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
>
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
>
> -----
>
> Session information updated at 2023-12-04 18:52
>
> INFO:root:Loading Scanpy libraries
>
> ERROR:root:For cellranger3-style .mtx files, please specify the
directory,
> not the .mtx.gz file name
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Friday, December 1, 2023 at 12:03 PM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Yes try cbScanpy ! It does exactly that !
>
> On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
>
> > Hi…Thanks again for your response. I’m trying to setup a somehow
generic
> > process where I take a set of matrix.mtx, features.tsv and
barcodes.tsv
> > files and visualize them w/ the cellbrowser.
> > I’m not sure if that contains the UMAP coords and clustering or of
they
> > always will so that’s why I thought I had to go thru’ Seurat but if
not
> > needed and you can point me to an example on how to go directly to the
> > cellbrowser I’d really appreciate.
> >
> > In the meantime I’ll try to see if I can get the cbScanpy to work w/
> these
> > files!
> > Thanks!
> > Alejandro.
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Friday, December 1, 2023 at 6:53 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> > didn't see that, I was convinced that you're using cbImportSeurat.
> >
> > I haven't tested cbSeurat in a long time! I should probably retire it.
> >
> > Don't you have umap coordinates etc as tsv files? If so, you can go
> > directly to cbBuild.
> >
> > If you need UMAP coords and clustering and cluster markers, and these
> > things are not already there in the meta or separate tsv files, you
can
> > also use cbScanpy, which at this point has had a ton more testing.
> >
> > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> >
> > > Hi….The problem is that I’m having a lot of errors when trying to
> > install
> > > Seurat 3 or 4. I was able to do it before but seem like it’s failing
> > now.
> > > Question: Is there a way of going from the matrix.mtx, features.tsv
> and
> > > barcodes.tsv directly into the cellbrowser w/o converting to Seurat?
> > >
> > > Thanks!
> > > Alejandro.
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> > matrix
> > > ?
> > > Probably I’ll need to install Seurat5. Can you try it on Seurat 3 or
4
> ?
> > >
> > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > >
> > > > Hi,
> > > > I’ve been building my cellbrowsers for matrix files for a while
now
> > and
> > > > was working fine but after some update the pipeline doesn’t seem
to
> be
> > > > working any more.
> > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > features.tsv.gz to the cellbrowser by first building the
> > > exprMatrix.tsv.gz
> > > > using “cbTool mtx2tsv …” and that step seem to work but then next
> step
> > > > cbSeurat is failing.
> > > > Any idea what can be the problem? Is it a problem of using Seurat
> > 5.0.0
> > > w/
> > > > latest version of cellbrowser?
> > > > Thanks!
> > > > Alejandro.
> > > > ------------------------------
> > > >
> > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > INFO:root:Wrote R script to
> > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > INFO:root:running
> /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > through Rscript
> > > > Seurat loaded, version 5.0.0
> > > > [1] "Seurat: Reading data"
> > > > [1] "Seurat: Reading data"
> > > > [1] "Loading input data matrix"
> > > > [1] "Loading tsv file with read.delim"
> > > > [1] "Seurat: Setup"
> > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
min.genes
> =
> > > > 200) :
> > > > argument "counts" is missing, with no default
> > > > Execution halted
> > > >
> > > > real 1m33.191s
> > > > user 1m17.847s
> > > > sys 0m1.896s
> > > > INFO:root:Wrote logfile of R run to
> > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > ERROR:root:R script did not complete successfully. Check
> > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > analysisLog.txt.
> > > >
> > > > —
> > > > Reply to this email directly, view it on GitHub
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Ah, it's just that file. Yes, we do test and it works for me.
This looks a little like a problem with your scanpy installation... but
we'll see.
I'm using Python 3.7 and Scanpy 1.9.2 and scipy 1.7.3
I can try to use the same versions that you have. Can you send me the list
of these versions: Python, Scipy, Numpy and especially Scanpy.
…On Tue, Dec 5, 2023 at 4:11 PM bugacov ***@***.***> wrote:
wget
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz
<
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> -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz
><
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Sent from my iPhone
On Dec 5, 2023, at 1:15 AM, Maximilian Haeussler ***@***.***> wrote:
Great, so this almost worked, it's only stuck at the markers calculation
step at the end now. This should be easy to fix.
You're using Python 3.9 from 2020 and combine that with the most recent
scanpy version, just a few weeks old. We didn't test this combination. You
could downgrade scanpy to a few versions older. But yes, it should
normally
work, it's possible I have to add yet another workaround (I've kept adding
workarounds for the different scanpy versions, every few months, something
is breaking there).
As soon as I can reproduce this error, I can fix it. Can you tell me where
you downloaded the mtx file from? Is this your own file or a 10X pbmc demo
file?
On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
> I actually uninstall cellbrowser and installed it again and now is doing
a
> bit more but still throwing errors:
>
>
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
> cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> pbmc3k
> INFO:root:Loading Scanpy libraries
> INFO:root:Creating scanpyOut
> INFO:root:Loading Scanpy libraries
> INFO:root:cbScanpy $Id$
> INFO:root:Command: /usr/local/bin/cbScanpy -e
> filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
> INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
> INFO:root:Restricting OPENBLAS to 4 threads
> INFO:root:Start time: 2023-12-05 04:30:26.199478
> -----
> anndata 0.10.3
> scanpy 1.9.6
> -----
> PIL 10.0.0
> asciitree NA
> cellbrowser v1.2.3
> cffi 1.14.5
> colorama 0.4.4
> cycler 0.12.1
> cython_runtime NA
> dateutil 2.8.2
> entrypoints 0.4
> exceptiongroup 1.2.0
> fasteners 0.18
> get_annotations NA
> h5py 3.10.0
> igraph 0.10.8
> importlib_resources NA
> joblib 1.3.2
> kiwisolver 1.4.5
> llvmlite 0.41.1
> louvain 0.8.1
> matplotlib 3.8.2
> mpl_toolkits NA
> natsort 8.4.0
> numba 0.58.1
> numcodecs 0.11.0
> numpy 1.25.2
> packaging 23.1
> pandas 2.1.3
> pkg_resources NA
> psutil 5.8.0
> pyparsing 3.1.1
> pytz 2021.1
> scipy 1.11.3
> session_info 1.0.0
> setuptools_scm NA
> six 1.15.0
> sklearn 1.3.2
> texttable 1.7.0
> threadpoolctl 3.2.0
> typing_extensions NA
> yaml 5.4.1
> zarr 2.16.1
> zipp NA
> zoneinfo NA
> -----
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> -----
> Session information updated at 2023-12-05 04:30
> INFO:root:Loading Scanpy libraries
> INFO:root:Loading expression matrix: mtx format
> INFO:root:Data has 2700 samples/observations
> INFO:root:Data has 32738 genes/variables
> INFO:root:Basic filtering: keep only cells with min 200 genes
> INFO:root:Basic filtering: keep only gene with min 3 cells
> INFO:root:After filtering: Data has 2700 samples/observations and 13714
> genes/variables
> INFO:root:Making gene names unique
> INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
> INFO:root:Auto-detected gene IDs type: symbols
> INFO:root:Remove cells with more than 0.050000 percent of mitochondrial
> genes
> INFO:root:Computing percentage of mitochondrial genes
> WARNING: saving figure to file scanpyOut/figs/violin.png
> INFO:root:Remove cells with less than 10 and more than 15000 genes
> INFO:root:Keeping only cells with < 15000 genes
> INFO:root:After filtering: Data has 2643 samples/observations and 13714
> genes/variables
> INFO:root:Keeping only cells with > 10 genes
> INFO:root:After filtering: Data has 2643 samples/observations and 13714
> genes/variables
> INFO:root:Expression normalization, counts per cell = 10000
> INFO:root:Did log2'ing of data
> INFO:root:Finding highly variable genes
> WARNING: saving figure to file
scanpyOut/figs/filter_genes_dispersion.png
> INFO:root:After high-var filtering: Data has 2643 samples/observations
and
> 1844 genes/variables
> INFO:root:Regressing out percent_mito and number of UMIs
> INFO:root:Scaling data, max_value=10
> INFO:root:Performing initial PCA, number of PCs: 100
> WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
> INFO:root:Estimating number of useful PCs based on Shekar et al, Cell
2016
> INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
> INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8<
https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=LRCerhXenZ3f2SWEPhr8kULBEGklU2NYVJ-O5nUQ-tA&e=>,
> STAR methods
> INFO:root:7 PCs will be used for tSNE and clustering
> INFO:root:Performing tSNE
> INFO:root:Running knn, using 7 PCs and 6 neighbors
> INFO:root:Performing Louvain Clustering, resolution 1.000000
> INFO:root:Found 13 louvain clusters
> INFO:root:Using cluster annotation from field: louvain
> WARNING: saving figure to file scanpyOut/figs/tsne.png
> INFO:root:Performing UMAP
> INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
> INFO:root:Finding top markers for each cluster
> INFO:root:Loading Scanpy libraries
> Traceback (most recent call last):
> File "/usr/local/bin/cbScanpy", line 8, in <module>
> sys.exit(cbScanpyCli())
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 6643, in cbScanpyCli
> adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> figDir, logFname, skipMarkers)
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 6432, in cbScanpy
> adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 4651, in runSafeRankGenesGroups
> clusterCellCounts =
> list(adata.obs.groupby([clusterField]).apply(len).iteritems())
> File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
> line 6204, in __getattr__
> return object.__getattribute__(self, name)
> AttributeError: 'Series' object has no attribute 'iteritems'
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
>
>
>
>
>
> From: Alejandro Bugacov ***@***.***>
> Date: Monday, December 4, 2023 at 7:49 PM
> To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> ***@***.***>
> Cc: Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Hi….I tried to run it on the example files from Scanpy example given
here
> https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html<
https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=fwTJ3jAfqNQubzg5eA4igcNVVQaoKw84DwvDYjI16tM&e=>
>
> wget
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=>
> -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz
><
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=>
>
>
> and I cannot get cbScanpy to run on them.
>
> I built the .h5ad file in python using
>
> import numpy as np
> import pandas as pd
> import scanpy as sc
>
> adata = sc.read_10x_mtx(
> 'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx`
> file
> var_names='gene_symbols', # use gene symbols for the variable names
> (variables-axis index)
> cache=True) # write a cache file for faster subsequent reading
>
> adata
>
>
> and then tried to run the
>
> cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
> pbmc3kImportScanpy
>
> But that give errors too.
>
> I
>
>
> From: Alejandro Bugacov ***@***.***>
> Date: Monday, December 4, 2023 at 11:36 AM
> To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> ***@***.***>
> Cc: Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> I’m not sure if I follow. Your example online points to a file
>
> cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> pbmc3k
>
> But what you mean here is that I need to put all 3 files under a folder
> and use that name convention?
> So I put all 3 files in a folder
>
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
> test1/
> total 106608
> -rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
> -rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
> -rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
>
> And then tried passing the folder name but I get error like below seems
> like is looking for the h5ad file?
>
>
>
> cbScanpy -e test1 -o scanpyOut -n testOut
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:cbScanpy $Id$
>
> INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
> testOut
>
> INFO:root:Matrix input file: test1
>
> INFO:root:Restricting OPENBLAS to 4 threads
>
> INFO:root:Start time: 2023-12-04 19:31:04.112141
>
> -----
>
> anndata 0.10.3
>
> scanpy 1.9.6
>
> -----
>
> PIL 10.0.0
>
> asciitree NA
>
> cellbrowser v1.0.1
>
> cffi 1.14.5
>
> colorama 0.4.4
>
> cycler 0.12.1
>
> cython_runtime NA
>
> dateutil 2.8.2
>
> entrypoints 0.4
>
> exceptiongroup 1.2.0
>
> fasteners 0.18
>
> get_annotations NA
>
> h5py 3.10.0
>
> igraph 0.10.8
>
> importlib_resources NA
>
> joblib 1.3.2
>
> kiwisolver 1.4.5
>
> llvmlite 0.41.1
>
> louvain 0.8.1
>
> matplotlib 3.8.2
>
> mpl_toolkits NA
>
> natsort 8.4.0
>
> numba 0.58.1
>
> numcodecs 0.11.0
>
> numpy 1.25.2
>
> packaging 23.1
>
> pandas 2.1.3
>
> pkg_resources NA
>
> psutil 5.8.0
>
> pyparsing 3.1.1
>
> pytz 2021.1
>
> scipy 1.11.3
>
> session_info 1.0.0
>
> setuptools_scm NA
>
> six 1.15.0
>
> sklearn 1.3.2
>
> texttable 1.7.0
>
> threadpoolctl 3.2.0
>
> typing_extensions NA
>
> yaml 5.4.1
>
> zarr 2.16.1
>
> zipp NA
>
> zoneinfo NA
>
> -----
>
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
>
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
>
> -----
>
> Session information updated at 2023-12-04 19:31
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading expression matrix: mtx format
>
> Traceback (most recent call last):
>
> File "/usr/local/bin/cbScanpy", line 8, in <module>
>
> sys.exit(cbScanpyCli())
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 5865, in cbScanpyCli
>
> adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> figDir, logFname)
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 5407, in cbScanpy
>
> adata = readMatrixAnndata(matrixFname,
> samplesOnRows=options.samplesOnRows, genome=options.genome)
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 4803, in readMatrixAnndata
>
> adata = sc.read(matrixFname, cache=False).T
>
> File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line
> 127, in read
>
> raise ValueError(
>
> ValueError: Reading with filekey 'test1' failed, the inferred filename
> PosixPath('write/test1.h5ad') does not exist. If you intended to provide
a
> filename, either use a filename ending on one of the available
extensions
> {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad',
> 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
>
>
>
>
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Monday, December 4, 2023 at 11:15 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Yes, the error is because your filenames don't follow the usual
> convention.
> Can you rename your files to matrix.mtx.gz and features.tsv.gz and
> barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
> again.
>
> I am not sure how/if I can solve this, this is a problem in scanpy, as
it
> only accepts the directory name, I think.
>
> On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
>
> > Hi….with the 2 mtx.gz files that I tried I did
> >
> >
> >
> > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> >
> >
> >
> > and get that need to specify a dir and not the mtx file for
> > cellranger3-style .mtx
> >
> > I tried passing the name of a folder w/ the files but didn’t work
> either.
> >
> > Can these mtx files be ran by with scanpy?
> >
> > Thanks,
> >
> > Alejandro.
> >
> > --------------------------
> >
> >
> >
> > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:cbScanpy $Id$
> >
> > INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> > scanpyOut -n test1
> >
> > INFO:root:Matrix input file: bates_matrix.mtx.gz
> >
> > INFO:root:Restricting OPENBLAS to 4 threads
> >
> > INFO:root:Start time: 2023-12-04 18:52:21.201824
> >
> > -----
> >
> > anndata 0.10.3
> >
> > scanpy 1.9.6
> >
> > -----
> >
> > PIL 10.0.0
> >
> > asciitree NA
> >
> > cellbrowser v1.0.1
> >
> > cffi 1.14.5
> >
> > colorama 0.4.4
> >
> > cycler 0.12.1
> >
> > cython_runtime NA
> >
> > dateutil 2.8.2
> >
> > entrypoints 0.4
> >
> > exceptiongroup 1.2.0
> >
> > fasteners 0.18
> >
> > get_annotations NA
> >
> > h5py 3.10.0
> >
> > igraph 0.10.8
> >
> > importlib_resources NA
> >
> > joblib 1.3.2
> >
> > kiwisolver 1.4.5
> >
> > llvmlite 0.41.1
> >
> > louvain 0.8.1
> >
> > matplotlib 3.8.2
> >
> > mpl_toolkits NA
> >
> > natsort 8.4.0
> >
> > numba 0.58.1
> >
> > numcodecs 0.11.0
> >
> > numpy 1.25.2
> >
> > packaging 23.1
> >
> > pandas 2.1.3
> >
> > pkg_resources NA
> >
> > psutil 5.8.0
> >
> > pyparsing 3.1.1
> >
> > pytz 2021.1
> >
> > scipy 1.11.3
> >
> > session_info 1.0.0
> >
> > setuptools_scm NA
> >
> > six 1.15.0
> >
> > sklearn 1.3.2
> >
> > texttable 1.7.0
> >
> > threadpoolctl 3.2.0
> >
> > typing_extensions NA
> >
> > yaml 5.4.1
> >
> > zarr 2.16.1
> >
> > zipp NA
> >
> > zoneinfo NA
> >
> > -----
> >
> > Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red
Hat
> > 11.4.1-2)]
> >
> > Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> >
> > -----
> >
> > Session information updated at 2023-12-04 18:52
> >
> > INFO:root:Loading Scanpy libraries
> >
> > ERROR:root:For cellranger3-style .mtx files, please specify the
> directory,
> > not the .mtx.gz file name
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Friday, December 1, 2023 at 12:03 PM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Yes try cbScanpy ! It does exactly that !
> >
> > On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> >
> > > Hi…Thanks again for your response. I’m trying to setup a somehow
> generic
> > > process where I take a set of matrix.mtx, features.tsv and
> barcodes.tsv
> > > files and visualize them w/ the cellbrowser.
> > > I’m not sure if that contains the UMAP coords and clustering or of
> they
> > > always will so that’s why I thought I had to go thru’ Seurat but if
> not
> > > needed and you can point me to an example on how to go directly to
the
> > > cellbrowser I’d really appreciate.
> > >
> > > In the meantime I’ll try to see if I can get the cbScanpy to work w/
> > these
> > > files!
> > > Thanks!
> > > Alejandro.
> > >
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Friday, December 1, 2023 at 6:53 AM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> > > didn't see that, I was convinced that you're using cbImportSeurat.
> > >
> > > I haven't tested cbSeurat in a long time! I should probably retire
it.
> > >
> > > Don't you have umap coordinates etc as tsv files? If so, you can go
> > > directly to cbBuild.
> > >
> > > If you need UMAP coords and clustering and cluster markers, and
these
> > > things are not already there in the meta or separate tsv files, you
> can
> > > also use cbScanpy, which at this point has had a ton more testing.
> > >
> > > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> > >
> > > > Hi….The problem is that I’m having a lot of errors when trying to
> > > install
> > > > Seurat 3 or 4. I was able to do it before but seem like it’s
failing
> > > now.
> > > > Question: Is there a way of going from the matrix.mtx,
features.tsv
> > and
> > > > barcodes.tsv directly into the cellbrowser w/o converting to
Seurat?
> > > >
> > > > Thanks!
> > > > Alejandro.
> > > >
> > > > From: Maximilian Haeussler ***@***.***>
> > > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > > To: maximilianh/cellBrowser ***@***.***>
> > > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > > argument
> > > > "counts" is missing, with no default (Issue #265)
> > > >
> > > > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> > > matrix
> > > > ?
> > > > Probably I’ll need to install Seurat5. Can you try it on Seurat 3
or
> 4
> > ?
> > > >
> > > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > > >
> > > > > Hi,
> > > > > I’ve been building my cellbrowsers for matrix files for a while
> now
> > > and
> > > > > was working fine but after some update the pipeline doesn’t seem
> to
> > be
> > > > > working any more.
> > > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > > features.tsv.gz to the cellbrowser by first building the
> > > > exprMatrix.tsv.gz
> > > > > using “cbTool mtx2tsv …” and that step seem to work but then
next
> > step
> > > > > cbSeurat is failing.
> > > > > Any idea what can be the problem? Is it a problem of using
Seurat
> > > 5.0.0
> > > > w/
> > > > > latest version of cellbrowser?
> > > > > Thanks!
> > > > > Alejandro.
> > > > > ------------------------------
> > > > >
> > > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > > INFO:root:Wrote R script to
> > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > INFO:root:running
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > through Rscript
> > > > > Seurat loaded, version 5.0.0
> > > > > [1] "Seurat: Reading data"
> > > > > [1] "Seurat: Reading data"
> > > > > [1] "Loading input data matrix"
> > > > > [1] "Loading tsv file with read.delim"
> > > > > [1] "Seurat: Setup"
> > > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
> min.genes
> > =
> > > > > 200) :
> > > > > argument "counts" is missing, with no default
> > > > > Execution halted
> > > > >
> > > > > real 1m33.191s
> > > > > user 1m17.847s
> > > > > sys 0m1.896s
> > > > > INFO:root:Wrote logfile of R run to
> > > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > > ERROR:root:R script did not complete successfully. Check
> > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > > analysisLog.txt.
> > > > >
> > > > > —
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From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Tuesday, December 5, 2023 at 7:23 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Ah, it's just that file. Yes, we do test and it works for me.
This looks a little like a problem with your scanpy installation... but
we'll see.
I'm using Python 3.7 and Scanpy 1.9.2 and scipy 1.7.3
I can try to use the same versions that you have. Can you send me the list
of these versions: Python, Scipy, Numpy and especially Scanpy.
Python 3.9.18
scanpy==1.9.6
scipy==1.11.3
numpy==1.25.2
Thanks!
Alejandro.
On Tue, Dec 5, 2023 at 4:11 PM bugacov ***@***.***> wrote:
wget
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=vfqy0VZ_lZZYeWdNabrBSDEqpde9StRJR_FA1l6CILg&e=>
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=%3E
> -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=R827nUTL2RtYc_UutyP-51nWeHNYrD9Y0d0nnCisuhc&e=>
><
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=%3E
Sent from my iPhone
On Dec 5, 2023, at 1:15 AM, Maximilian Haeussler ***@***.***> wrote:
Great, so this almost worked, it's only stuck at the markers calculation
step at the end now. This should be easy to fix.
You're using Python 3.9 from 2020 and combine that with the most recent
scanpy version, just a few weeks old. We didn't test this combination. You
could downgrade scanpy to a few versions older. But yes, it should
normally
work, it's possible I have to add yet another workaround (I've kept adding
workarounds for the different scanpy versions, every few months, something
is breaking there).
As soon as I can reproduce this error, I can fix it. Can you tell me where
you downloaded the mtx file from? Is this your own file or a 10X pbmc demo
file?
On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
> I actually uninstall cellbrowser and installed it again and now is doing
a
> bit more but still throwing errors:
>
>
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
> cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> pbmc3k
> INFO:root:Loading Scanpy libraries
> INFO:root:Creating scanpyOut
> INFO:root:Loading Scanpy libraries
> INFO:root:cbScanpy $Id$
> INFO:root:Command: /usr/local/bin/cbScanpy -e
> filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
> INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
> INFO:root:Restricting OPENBLAS to 4 threads
> INFO:root:Start time: 2023-12-05 04:30:26.199478
> -----
> anndata 0.10.3
> scanpy 1.9.6
> -----
> PIL 10.0.0
> asciitree NA
> cellbrowser v1.2.3
> cffi 1.14.5
> colorama 0.4.4
> cycler 0.12.1
> cython_runtime NA
> dateutil 2.8.2
> entrypoints 0.4
> exceptiongroup 1.2.0
> fasteners 0.18
> get_annotations NA
> h5py 3.10.0
> igraph 0.10.8
> importlib_resources NA
> joblib 1.3.2
> kiwisolver 1.4.5
> llvmlite 0.41.1
> louvain 0.8.1
> matplotlib 3.8.2
> mpl_toolkits NA
> natsort 8.4.0
> numba 0.58.1
> numcodecs 0.11.0
> numpy 1.25.2
> packaging 23.1
> pandas 2.1.3
> pkg_resources NA
> psutil 5.8.0
> pyparsing 3.1.1
> pytz 2021.1
> scipy 1.11.3
> session_info 1.0.0
> setuptools_scm NA
> six 1.15.0
> sklearn 1.3.2
> texttable 1.7.0
> threadpoolctl 3.2.0
> typing_extensions NA
> yaml 5.4.1
> zarr 2.16.1
> zipp NA
> zoneinfo NA
> -----
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> -----
> Session information updated at 2023-12-05 04:30
> INFO:root:Loading Scanpy libraries
> INFO:root:Loading expression matrix: mtx format
> INFO:root:Data has 2700 samples/observations
> INFO:root:Data has 32738 genes/variables
> INFO:root:Basic filtering: keep only cells with min 200 genes
> INFO:root:Basic filtering: keep only gene with min 3 cells
> INFO:root:After filtering: Data has 2700 samples/observations and 13714
> genes/variables
> INFO:root:Making gene names unique
> INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
> INFO:root:Auto-detected gene IDs type: symbols
> INFO:root:Remove cells with more than 0.050000 percent of mitochondrial
> genes
> INFO:root:Computing percentage of mitochondrial genes
> WARNING: saving figure to file scanpyOut/figs/violin.png
> INFO:root:Remove cells with less than 10 and more than 15000 genes
> INFO:root:Keeping only cells with < 15000 genes
> INFO:root:After filtering: Data has 2643 samples/observations and 13714
> genes/variables
> INFO:root:Keeping only cells with > 10 genes
> INFO:root:After filtering: Data has 2643 samples/observations and 13714
> genes/variables
> INFO:root:Expression normalization, counts per cell = 10000
> INFO:root:Did log2'ing of data
> INFO:root:Finding highly variable genes
> WARNING: saving figure to file
scanpyOut/figs/filter_genes_dispersion.png
> INFO:root:After high-var filtering: Data has 2643 samples/observations
and
> 1844 genes/variables
> INFO:root:Regressing out percent_mito and number of UMIs
> INFO:root:Scaling data, max_value=10
> INFO:root:Performing initial PCA, number of PCs: 100
> WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
> INFO:root:Estimating number of useful PCs based on Shekar et al, Cell
2016
> INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
> INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8<<https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=V7ZgmTdvAWsVTOnGdosk-ZKl0Rd7rUdm2Pt_Q236vTI&e=>
https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=LRCerhXenZ3f2SWEPhr8kULBEGklU2NYVJ-O5nUQ-tA&e=%3E,
> STAR methods
> INFO:root:7 PCs will be used for tSNE and clustering
> INFO:root:Performing tSNE
> INFO:root:Running knn, using 7 PCs and 6 neighbors
> INFO:root:Performing Louvain Clustering, resolution 1.000000
> INFO:root:Found 13 louvain clusters
> INFO:root:Using cluster annotation from field: louvain
> WARNING: saving figure to file scanpyOut/figs/tsne.png
> INFO:root:Performing UMAP
> INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
> INFO:root:Finding top markers for each cluster
> INFO:root:Loading Scanpy libraries
> Traceback (most recent call last):
> File "/usr/local/bin/cbScanpy", line 8, in <module>
> sys.exit(cbScanpyCli())
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 6643, in cbScanpyCli
> adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> figDir, logFname, skipMarkers)
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 6432, in cbScanpy
> adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 4651, in runSafeRankGenesGroups
> clusterCellCounts =
> list(adata.obs.groupby([clusterField]).apply(len).iteritems())
> File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
> line 6204, in __getattr__
> return object.__getattribute__(self, name)
> AttributeError: 'Series' object has no attribute 'iteritems'
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
>
>
>
>
>
> From: Alejandro Bugacov ***@***.***>
> Date: Monday, December 4, 2023 at 7:49 PM
> To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> ***@***.***>
> Cc: Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Hi….I tried to run it on the example files from Scanpy example given
here
> https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html<<https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=hkV8fjmu18Vu9JP99fI2Yr2oNegSCXgjEAuaMlSN-ps&e=>
https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=fwTJ3jAfqNQubzg5eA4igcNVVQaoKw84DwvDYjI16tM&e=%3E
>
> wget
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=vfqy0VZ_lZZYeWdNabrBSDEqpde9StRJR_FA1l6CILg&e=>
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=%3E
> -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=R827nUTL2RtYc_UutyP-51nWeHNYrD9Y0d0nnCisuhc&e=>
><
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=%3E
>
>
> and I cannot get cbScanpy to run on them.
>
> I built the .h5ad file in python using
>
> import numpy as np
> import pandas as pd
> import scanpy as sc
>
> adata = sc.read_10x_mtx(
> 'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx`
> file
> var_names='gene_symbols', # use gene symbols for the variable names
> (variables-axis index)
> cache=True) # write a cache file for faster subsequent reading
>
> adata
>
>
> and then tried to run the
>
> cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
> pbmc3kImportScanpy
>
> But that give errors too.
>
> I
>
>
> From: Alejandro Bugacov ***@***.***>
> Date: Monday, December 4, 2023 at 11:36 AM
> To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> ***@***.***>
> Cc: Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> I’m not sure if I follow. Your example online points to a file
>
> cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> pbmc3k
>
> But what you mean here is that I need to put all 3 files under a folder
> and use that name convention?
> So I put all 3 files in a folder
>
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
> test1/
> total 106608
> -rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
> -rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
> -rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
>
> And then tried passing the folder name but I get error like below seems
> like is looking for the h5ad file?
>
>
>
> cbScanpy -e test1 -o scanpyOut -n testOut
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:cbScanpy $Id$
>
> INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
> testOut
>
> INFO:root:Matrix input file: test1
>
> INFO:root:Restricting OPENBLAS to 4 threads
>
> INFO:root:Start time: 2023-12-04 19:31:04.112141
>
> -----
>
> anndata 0.10.3
>
> scanpy 1.9.6
>
> -----
>
> PIL 10.0.0
>
> asciitree NA
>
> cellbrowser v1.0.1
>
> cffi 1.14.5
>
> colorama 0.4.4
>
> cycler 0.12.1
>
> cython_runtime NA
>
> dateutil 2.8.2
>
> entrypoints 0.4
>
> exceptiongroup 1.2.0
>
> fasteners 0.18
>
> get_annotations NA
>
> h5py 3.10.0
>
> igraph 0.10.8
>
> importlib_resources NA
>
> joblib 1.3.2
>
> kiwisolver 1.4.5
>
> llvmlite 0.41.1
>
> louvain 0.8.1
>
> matplotlib 3.8.2
>
> mpl_toolkits NA
>
> natsort 8.4.0
>
> numba 0.58.1
>
> numcodecs 0.11.0
>
> numpy 1.25.2
>
> packaging 23.1
>
> pandas 2.1.3
>
> pkg_resources NA
>
> psutil 5.8.0
>
> pyparsing 3.1.1
>
> pytz 2021.1
>
> scipy 1.11.3
>
> session_info 1.0.0
>
> setuptools_scm NA
>
> six 1.15.0
>
> sklearn 1.3.2
>
> texttable 1.7.0
>
> threadpoolctl 3.2.0
>
> typing_extensions NA
>
> yaml 5.4.1
>
> zarr 2.16.1
>
> zipp NA
>
> zoneinfo NA
>
> -----
>
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
>
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
>
> -----
>
> Session information updated at 2023-12-04 19:31
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading expression matrix: mtx format
>
> Traceback (most recent call last):
>
> File "/usr/local/bin/cbScanpy", line 8, in <module>
>
> sys.exit(cbScanpyCli())
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 5865, in cbScanpyCli
>
> adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> figDir, logFname)
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 5407, in cbScanpy
>
> adata = readMatrixAnndata(matrixFname,
> samplesOnRows=options.samplesOnRows, genome=options.genome)
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 4803, in readMatrixAnndata
>
> adata = sc.read(matrixFname, cache=False).T
>
> File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line
> 127, in read
>
> raise ValueError(
>
> ValueError: Reading with filekey 'test1' failed, the inferred filename
> PosixPath('write/test1.h5ad') does not exist. If you intended to provide
a
> filename, either use a filename ending on one of the available
extensions
> {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad',
> 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
>
>
>
>
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Monday, December 4, 2023 at 11:15 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Yes, the error is because your filenames don't follow the usual
> convention.
> Can you rename your files to matrix.mtx.gz and features.tsv.gz and
> barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
> again.
>
> I am not sure how/if I can solve this, this is a problem in scanpy, as
it
> only accepts the directory name, I think.
>
> On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
>
> > Hi….with the 2 mtx.gz files that I tried I did
> >
> >
> >
> > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> >
> >
> >
> > and get that need to specify a dir and not the mtx file for
> > cellranger3-style .mtx
> >
> > I tried passing the name of a folder w/ the files but didn’t work
> either.
> >
> > Can these mtx files be ran by with scanpy?
> >
> > Thanks,
> >
> > Alejandro.
> >
> > --------------------------
> >
> >
> >
> > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:cbScanpy $Id$
> >
> > INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> > scanpyOut -n test1
> >
> > INFO:root:Matrix input file: bates_matrix.mtx.gz
> >
> > INFO:root:Restricting OPENBLAS to 4 threads
> >
> > INFO:root:Start time: 2023-12-04 18:52:21.201824
> >
> > -----
> >
> > anndata 0.10.3
> >
> > scanpy 1.9.6
> >
> > -----
> >
> > PIL 10.0.0
> >
> > asciitree NA
> >
> > cellbrowser v1.0.1
> >
> > cffi 1.14.5
> >
> > colorama 0.4.4
> >
> > cycler 0.12.1
> >
> > cython_runtime NA
> >
> > dateutil 2.8.2
> >
> > entrypoints 0.4
> >
> > exceptiongroup 1.2.0
> >
> > fasteners 0.18
> >
> > get_annotations NA
> >
> > h5py 3.10.0
> >
> > igraph 0.10.8
> >
> > importlib_resources NA
> >
> > joblib 1.3.2
> >
> > kiwisolver 1.4.5
> >
> > llvmlite 0.41.1
> >
> > louvain 0.8.1
> >
> > matplotlib 3.8.2
> >
> > mpl_toolkits NA
> >
> > natsort 8.4.0
> >
> > numba 0.58.1
> >
> > numcodecs 0.11.0
> >
> > numpy 1.25.2
> >
> > packaging 23.1
> >
> > pandas 2.1.3
> >
> > pkg_resources NA
> >
> > psutil 5.8.0
> >
> > pyparsing 3.1.1
> >
> > pytz 2021.1
> >
> > scipy 1.11.3
> >
> > session_info 1.0.0
> >
> > setuptools_scm NA
> >
> > six 1.15.0
> >
> > sklearn 1.3.2
> >
> > texttable 1.7.0
> >
> > threadpoolctl 3.2.0
> >
> > typing_extensions NA
> >
> > yaml 5.4.1
> >
> > zarr 2.16.1
> >
> > zipp NA
> >
> > zoneinfo NA
> >
> > -----
> >
> > Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red
Hat
> > 11.4.1-2)]
> >
> > Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> >
> > -----
> >
> > Session information updated at 2023-12-04 18:52
> >
> > INFO:root:Loading Scanpy libraries
> >
> > ERROR:root:For cellranger3-style .mtx files, please specify the
> directory,
> > not the .mtx.gz file name
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Friday, December 1, 2023 at 12:03 PM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Yes try cbScanpy ! It does exactly that !
> >
> > On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> >
> > > Hi…Thanks again for your response. I’m trying to setup a somehow
> generic
> > > process where I take a set of matrix.mtx, features.tsv and
> barcodes.tsv
> > > files and visualize them w/ the cellbrowser.
> > > I’m not sure if that contains the UMAP coords and clustering or of
> they
> > > always will so that’s why I thought I had to go thru’ Seurat but if
> not
> > > needed and you can point me to an example on how to go directly to
the
> > > cellbrowser I’d really appreciate.
> > >
> > > In the meantime I’ll try to see if I can get the cbScanpy to work w/
> > these
> > > files!
> > > Thanks!
> > > Alejandro.
> > >
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Friday, December 1, 2023 at 6:53 AM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> > > didn't see that, I was convinced that you're using cbImportSeurat.
> > >
> > > I haven't tested cbSeurat in a long time! I should probably retire
it.
> > >
> > > Don't you have umap coordinates etc as tsv files? If so, you can go
> > > directly to cbBuild.
> > >
> > > If you need UMAP coords and clustering and cluster markers, and
these
> > > things are not already there in the meta or separate tsv files, you
> can
> > > also use cbScanpy, which at this point has had a ton more testing.
> > >
> > > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> > >
> > > > Hi….The problem is that I’m having a lot of errors when trying to
> > > install
> > > > Seurat 3 or 4. I was able to do it before but seem like it’s
failing
> > > now.
> > > > Question: Is there a way of going from the matrix.mtx,
features.tsv
> > and
> > > > barcodes.tsv directly into the cellbrowser w/o converting to
Seurat?
> > > >
> > > > Thanks!
> > > > Alejandro.
> > > >
> > > > From: Maximilian Haeussler ***@***.***>
> > > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > > To: maximilianh/cellBrowser ***@***.***>
> > > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > > argument
> > > > "counts" is missing, with no default (Issue #265)
> > > >
> > > > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> > > matrix
> > > > ?
> > > > Probably I’ll need to install Seurat5. Can you try it on Seurat 3
or
> 4
> > ?
> > > >
> > > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > > >
> > > > > Hi,
> > > > > I’ve been building my cellbrowsers for matrix files for a while
> now
> > > and
> > > > > was working fine but after some update the pipeline doesn’t seem
> to
> > be
> > > > > working any more.
> > > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > > features.tsv.gz to the cellbrowser by first building the
> > > > exprMatrix.tsv.gz
> > > > > using “cbTool mtx2tsv …” and that step seem to work but then
next
> > step
> > > > > cbSeurat is failing.
> > > > > Any idea what can be the problem? Is it a problem of using
Seurat
> > > 5.0.0
> > > > w/
> > > > > latest version of cellbrowser?
> > > > > Thanks!
> > > > > Alejandro.
> > > > > ------------------------------
> > > > >
> > > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > > INFO:root:Wrote R script to
> > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > INFO:root:running
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > through Rscript
> > > > > Seurat loaded, version 5.0.0
> > > > > [1] "Seurat: Reading data"
> > > > > [1] "Seurat: Reading data"
> > > > > [1] "Loading input data matrix"
> > > > > [1] "Loading tsv file with read.delim"
> > > > > [1] "Seurat: Setup"
> > > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
> min.genes
> > =
> > > > > 200) :
> > > > > argument "counts" is missing, with no default
> > > > > Execution halted
> > > > >
> > > > > real 1m33.191s
> > > > > user 1m17.847s
> > > > > sys 0m1.896s
> > > > > INFO:root:Wrote logfile of R run to
> > > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > > ERROR:root:R script did not complete successfully. Check
> > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > > analysisLog.txt.
> > > > >
> > > > > —
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#265><<<<<<https://urldefense.us/v2/url?u=https-3A__github.com_maximilianh_cellBrowser_issues_265-253E-253C-253C-253C-253C-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=3pEYc20R4ycfin4Ef-nJBNw8YaMypATa24Ei5VH876s&e=>
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Hi….I was wondering if you were able to reproduce my errors? I think that the main difference seems to be the Python version on my machine but I kinda constrained to stay on that version if possible.
Let me know if there’s something else I can try.
Again the versions in my system are:
Python 3.9.18
scanpy==1.9.6
scipy==1.11.3
numpy==1.25.2
Thanks!
Alejandro.
From: Alejandro Bugacov ***@***.***>
Date: Tuesday, December 5, 2023 at 2:34 PM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser ***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Tuesday, December 5, 2023 at 7:23 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument "counts" is missing, with no default (Issue #265)
Ah, it's just that file. Yes, we do test and it works for me.
This looks a little like a problem with your scanpy installation... but
we'll see.
I'm using Python 3.7 and Scanpy 1.9.2 and scipy 1.7.3
I can try to use the same versions that you have. Can you send me the list
of these versions: Python, Scipy, Numpy and especially Scanpy.
Python 3.9.18
scanpy==1.9.6
scipy==1.11.3
numpy==1.25.2
Thanks!
Alejandro.
On Tue, Dec 5, 2023 at 4:11 PM bugacov ***@***.***> wrote:
wget
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=vfqy0VZ_lZZYeWdNabrBSDEqpde9StRJR_FA1l6CILg&e=>
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=%3E
> -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=R827nUTL2RtYc_UutyP-51nWeHNYrD9Y0d0nnCisuhc&e=>
><
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=%3E
Sent from my iPhone
On Dec 5, 2023, at 1:15 AM, Maximilian Haeussler ***@***.***> wrote:
Great, so this almost worked, it's only stuck at the markers calculation
step at the end now. This should be easy to fix.
You're using Python 3.9 from 2020 and combine that with the most recent
scanpy version, just a few weeks old. We didn't test this combination. You
could downgrade scanpy to a few versions older. But yes, it should
normally
work, it's possible I have to add yet another workaround (I've kept adding
workarounds for the different scanpy versions, every few months, something
is breaking there).
As soon as I can reproduce this error, I can fix it. Can you tell me where
you downloaded the mtx file from? Is this your own file or a 10X pbmc demo
file?
On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
> I actually uninstall cellbrowser and installed it again and now is doing
a
> bit more but still throwing errors:
>
>
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
> cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> pbmc3k
> INFO:root:Loading Scanpy libraries
> INFO:root:Creating scanpyOut
> INFO:root:Loading Scanpy libraries
> INFO:root:cbScanpy $Id$
> INFO:root:Command: /usr/local/bin/cbScanpy -e
> filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
> INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
> INFO:root:Restricting OPENBLAS to 4 threads
> INFO:root:Start time: 2023-12-05 04:30:26.199478
> -----
> anndata 0.10.3
> scanpy 1.9.6
> -----
> PIL 10.0.0
> asciitree NA
> cellbrowser v1.2.3
> cffi 1.14.5
> colorama 0.4.4
> cycler 0.12.1
> cython_runtime NA
> dateutil 2.8.2
> entrypoints 0.4
> exceptiongroup 1.2.0
> fasteners 0.18
> get_annotations NA
> h5py 3.10.0
> igraph 0.10.8
> importlib_resources NA
> joblib 1.3.2
> kiwisolver 1.4.5
> llvmlite 0.41.1
> louvain 0.8.1
> matplotlib 3.8.2
> mpl_toolkits NA
> natsort 8.4.0
> numba 0.58.1
> numcodecs 0.11.0
> numpy 1.25.2
> packaging 23.1
> pandas 2.1.3
> pkg_resources NA
> psutil 5.8.0
> pyparsing 3.1.1
> pytz 2021.1
> scipy 1.11.3
> session_info 1.0.0
> setuptools_scm NA
> six 1.15.0
> sklearn 1.3.2
> texttable 1.7.0
> threadpoolctl 3.2.0
> typing_extensions NA
> yaml 5.4.1
> zarr 2.16.1
> zipp NA
> zoneinfo NA
> -----
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> -----
> Session information updated at 2023-12-05 04:30
> INFO:root:Loading Scanpy libraries
> INFO:root:Loading expression matrix: mtx format
> INFO:root:Data has 2700 samples/observations
> INFO:root:Data has 32738 genes/variables
> INFO:root:Basic filtering: keep only cells with min 200 genes
> INFO:root:Basic filtering: keep only gene with min 3 cells
> INFO:root:After filtering: Data has 2700 samples/observations and 13714
> genes/variables
> INFO:root:Making gene names unique
> INFO:root:'geneIdType' is not specified in config file or set to 'auto'.
> INFO:root:Auto-detected gene IDs type: symbols
> INFO:root:Remove cells with more than 0.050000 percent of mitochondrial
> genes
> INFO:root:Computing percentage of mitochondrial genes
> WARNING: saving figure to file scanpyOut/figs/violin.png
> INFO:root:Remove cells with less than 10 and more than 15000 genes
> INFO:root:Keeping only cells with < 15000 genes
> INFO:root:After filtering: Data has 2643 samples/observations and 13714
> genes/variables
> INFO:root:Keeping only cells with > 10 genes
> INFO:root:After filtering: Data has 2643 samples/observations and 13714
> genes/variables
> INFO:root:Expression normalization, counts per cell = 10000
> INFO:root:Did log2'ing of data
> INFO:root:Finding highly variable genes
> WARNING: saving figure to file
scanpyOut/figs/filter_genes_dispersion.png
> INFO:root:After high-var filtering: Data has 2643 samples/observations
and
> 1844 genes/variables
> INFO:root:Regressing out percent_mito and number of UMIs
> INFO:root:Scaling data, max_value=10
> INFO:root:Performing initial PCA, number of PCs: 100
> WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
> INFO:root:Estimating number of useful PCs based on Shekar et al, Cell
2016
> INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
> INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8<<https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=V7ZgmTdvAWsVTOnGdosk-ZKl0Rd7rUdm2Pt_Q236vTI&e=>
https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=LRCerhXenZ3f2SWEPhr8kULBEGklU2NYVJ-O5nUQ-tA&e=%3E,
> STAR methods
> INFO:root:7 PCs will be used for tSNE and clustering
> INFO:root:Performing tSNE
> INFO:root:Running knn, using 7 PCs and 6 neighbors
> INFO:root:Performing Louvain Clustering, resolution 1.000000
> INFO:root:Found 13 louvain clusters
> INFO:root:Using cluster annotation from field: louvain
> WARNING: saving figure to file scanpyOut/figs/tsne.png
> INFO:root:Performing UMAP
> INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
> INFO:root:Finding top markers for each cluster
> INFO:root:Loading Scanpy libraries
> Traceback (most recent call last):
> File "/usr/local/bin/cbScanpy", line 8, in <module>
> sys.exit(cbScanpyCli())
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 6643, in cbScanpyCli
> adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> figDir, logFname, skipMarkers)
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 6432, in cbScanpy
> adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 4651, in runSafeRankGenesGroups
> clusterCellCounts =
> list(adata.obs.groupby([clusterField]).apply(len).iteritems())
> File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
> line 6204, in __getattr__
> return object.__getattribute__(self, name)
> AttributeError: 'Series' object has no attribute 'iteritems'
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
>
>
>
>
>
> From: Alejandro Bugacov ***@***.***>
> Date: Monday, December 4, 2023 at 7:49 PM
> To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> ***@***.***>
> Cc: Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Hi….I tried to run it on the example files from Scanpy example given
here
> https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html<<https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=hkV8fjmu18Vu9JP99fI2Yr2oNegSCXgjEAuaMlSN-ps&e=>
https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=fwTJ3jAfqNQubzg5eA4igcNVVQaoKw84DwvDYjI16tM&e=%3E
>
> wget
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=vfqy0VZ_lZZYeWdNabrBSDEqpde9StRJR_FA1l6CILg&e=>
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=%3E
> -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz<https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=R827nUTL2RtYc_UutyP-51nWeHNYrD9Y0d0nnCisuhc&e=>
><
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=%3E
>
>
> and I cannot get cbScanpy to run on them.
>
> I built the .h5ad file in python using
>
> import numpy as np
> import pandas as pd
> import scanpy as sc
>
> adata = sc.read_10x_mtx(
> 'data/filtered_gene_bc_matrices/hg19/', # the directory with the `.mtx`
> file
> var_names='gene_symbols', # use gene symbols for the variable names
> (variables-axis index)
> cache=True) # write a cache file for faster subsequent reading
>
> adata
>
>
> and then tried to run the
>
> cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
> pbmc3kImportScanpy
>
> But that give errors too.
>
> I
>
>
> From: Alejandro Bugacov ***@***.***>
> Date: Monday, December 4, 2023 at 11:36 AM
> To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> ***@***.***>
> Cc: Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> I’m not sure if I follow. Your example online points to a file
>
> cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> pbmc3k
>
> But what you mean here is that I need to put all 3 files under a folder
> and use that name convention?
> So I put all 3 files in a folder
>
> facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
> test1/
> total 106608
> -rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
> -rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
> -rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
>
> And then tried passing the folder name but I get error like below seems
> like is looking for the h5ad file?
>
>
>
> cbScanpy -e test1 -o scanpyOut -n testOut
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:cbScanpy $Id$
>
> INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
> testOut
>
> INFO:root:Matrix input file: test1
>
> INFO:root:Restricting OPENBLAS to 4 threads
>
> INFO:root:Start time: 2023-12-04 19:31:04.112141
>
> -----
>
> anndata 0.10.3
>
> scanpy 1.9.6
>
> -----
>
> PIL 10.0.0
>
> asciitree NA
>
> cellbrowser v1.0.1
>
> cffi 1.14.5
>
> colorama 0.4.4
>
> cycler 0.12.1
>
> cython_runtime NA
>
> dateutil 2.8.2
>
> entrypoints 0.4
>
> exceptiongroup 1.2.0
>
> fasteners 0.18
>
> get_annotations NA
>
> h5py 3.10.0
>
> igraph 0.10.8
>
> importlib_resources NA
>
> joblib 1.3.2
>
> kiwisolver 1.4.5
>
> llvmlite 0.41.1
>
> louvain 0.8.1
>
> matplotlib 3.8.2
>
> mpl_toolkits NA
>
> natsort 8.4.0
>
> numba 0.58.1
>
> numcodecs 0.11.0
>
> numpy 1.25.2
>
> packaging 23.1
>
> pandas 2.1.3
>
> pkg_resources NA
>
> psutil 5.8.0
>
> pyparsing 3.1.1
>
> pytz 2021.1
>
> scipy 1.11.3
>
> session_info 1.0.0
>
> setuptools_scm NA
>
> six 1.15.0
>
> sklearn 1.3.2
>
> texttable 1.7.0
>
> threadpoolctl 3.2.0
>
> typing_extensions NA
>
> yaml 5.4.1
>
> zarr 2.16.1
>
> zipp NA
>
> zoneinfo NA
>
> -----
>
> Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red Hat
> 11.4.1-2)]
>
> Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
>
> -----
>
> Session information updated at 2023-12-04 19:31
>
> INFO:root:Loading Scanpy libraries
>
> INFO:root:Loading expression matrix: mtx format
>
> Traceback (most recent call last):
>
> File "/usr/local/bin/cbScanpy", line 8, in <module>
>
> sys.exit(cbScanpyCli())
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 5865, in cbScanpyCli
>
> adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> figDir, logFname)
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 5407, in cbScanpy
>
> adata = readMatrixAnndata(matrixFname,
> samplesOnRows=options.samplesOnRows, genome=options.genome)
>
> File
"/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> line 4803, in readMatrixAnndata
>
> adata = sc.read(matrixFname, cache=False).T
>
> File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py", line
> 127, in read
>
> raise ValueError(
>
> ValueError: Reading with filekey 'test1' failed, the inferred filename
> PosixPath('write/test1.h5ad') does not exist. If you intended to provide
a
> filename, either use a filename ending on one of the available
extensions
> {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv', 'h5ad',
> 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
>
>
>
>
>
>
> From: Maximilian Haeussler ***@***.***>
> Reply-To: maximilianh/cellBrowser ***@***.***>
> Date: Monday, December 4, 2023 at 11:15 AM
> To: maximilianh/cellBrowser ***@***.***>
> Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
argument
> "counts" is missing, with no default (Issue #265)
>
> Yes, the error is because your filenames don't follow the usual
> convention.
> Can you rename your files to matrix.mtx.gz and features.tsv.gz and
> barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
> again.
>
> I am not sure how/if I can solve this, this is a problem in scanpy, as
it
> only accepts the directory name, I think.
>
> On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
>
> > Hi….with the 2 mtx.gz files that I tried I did
> >
> >
> >
> > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> >
> >
> >
> > and get that need to specify a dir and not the mtx file for
> > cellranger3-style .mtx
> >
> > I tried passing the name of a folder w/ the files but didn’t work
> either.
> >
> > Can these mtx files be ran by with scanpy?
> >
> > Thanks,
> >
> > Alejandro.
> >
> > --------------------------
> >
> >
> >
> > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:cbScanpy $Id$
> >
> > INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> > scanpyOut -n test1
> >
> > INFO:root:Matrix input file: bates_matrix.mtx.gz
> >
> > INFO:root:Restricting OPENBLAS to 4 threads
> >
> > INFO:root:Start time: 2023-12-04 18:52:21.201824
> >
> > -----
> >
> > anndata 0.10.3
> >
> > scanpy 1.9.6
> >
> > -----
> >
> > PIL 10.0.0
> >
> > asciitree NA
> >
> > cellbrowser v1.0.1
> >
> > cffi 1.14.5
> >
> > colorama 0.4.4
> >
> > cycler 0.12.1
> >
> > cython_runtime NA
> >
> > dateutil 2.8.2
> >
> > entrypoints 0.4
> >
> > exceptiongroup 1.2.0
> >
> > fasteners 0.18
> >
> > get_annotations NA
> >
> > h5py 3.10.0
> >
> > igraph 0.10.8
> >
> > importlib_resources NA
> >
> > joblib 1.3.2
> >
> > kiwisolver 1.4.5
> >
> > llvmlite 0.41.1
> >
> > louvain 0.8.1
> >
> > matplotlib 3.8.2
> >
> > mpl_toolkits NA
> >
> > natsort 8.4.0
> >
> > numba 0.58.1
> >
> > numcodecs 0.11.0
> >
> > numpy 1.25.2
> >
> > packaging 23.1
> >
> > pandas 2.1.3
> >
> > pkg_resources NA
> >
> > psutil 5.8.0
> >
> > pyparsing 3.1.1
> >
> > pytz 2021.1
> >
> > scipy 1.11.3
> >
> > session_info 1.0.0
> >
> > setuptools_scm NA
> >
> > six 1.15.0
> >
> > sklearn 1.3.2
> >
> > texttable 1.7.0
> >
> > threadpoolctl 3.2.0
> >
> > typing_extensions NA
> >
> > yaml 5.4.1
> >
> > zarr 2.16.1
> >
> > zipp NA
> >
> > zoneinfo NA
> >
> > -----
> >
> > Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red
Hat
> > 11.4.1-2)]
> >
> > Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> >
> > -----
> >
> > Session information updated at 2023-12-04 18:52
> >
> > INFO:root:Loading Scanpy libraries
> >
> > ERROR:root:For cellranger3-style .mtx files, please specify the
> directory,
> > not the .mtx.gz file name
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Friday, December 1, 2023 at 12:03 PM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Yes try cbScanpy ! It does exactly that !
> >
> > On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> >
> > > Hi…Thanks again for your response. I’m trying to setup a somehow
> generic
> > > process where I take a set of matrix.mtx, features.tsv and
> barcodes.tsv
> > > files and visualize them w/ the cellbrowser.
> > > I’m not sure if that contains the UMAP coords and clustering or of
> they
> > > always will so that’s why I thought I had to go thru’ Seurat but if
> not
> > > needed and you can point me to an example on how to go directly to
the
> > > cellbrowser I’d really appreciate.
> > >
> > > In the meantime I’ll try to see if I can get the cbScanpy to work w/
> > these
> > > files!
> > > Thanks!
> > > Alejandro.
> > >
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Friday, December 1, 2023 at 6:53 AM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Wait... why are you running Seurat? you're running cbSeurat, Sorry I
> > > didn't see that, I was convinced that you're using cbImportSeurat.
> > >
> > > I haven't tested cbSeurat in a long time! I should probably retire
it.
> > >
> > > Don't you have umap coordinates etc as tsv files? If so, you can go
> > > directly to cbBuild.
> > >
> > > If you need UMAP coords and clustering and cluster markers, and
these
> > > things are not already there in the meta or separate tsv files, you
> can
> > > also use cbScanpy, which at this point has had a ton more testing.
> > >
> > > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> > >
> > > > Hi….The problem is that I’m having a lot of errors when trying to
> > > install
> > > > Seurat 3 or 4. I was able to do it before but seem like it’s
failing
> > > now.
> > > > Question: Is there a way of going from the matrix.mtx,
features.tsv
> > and
> > > > barcodes.tsv directly into the cellbrowser w/o converting to
Seurat?
> > > >
> > > > Thanks!
> > > > Alejandro.
> > > >
> > > > From: Maximilian Haeussler ***@***.***>
> > > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > > To: maximilianh/cellBrowser ***@***.***>
> > > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > > argument
> > > > "counts" is missing, with no default (Issue #265)
> > > >
> > > > Hm yes I don’t think I’ve tested on Seurat. Do you want share your
> > > matrix
> > > > ?
> > > > Probably I’ll need to install Seurat5. Can you try it on Seurat 3
or
> 4
> > ?
> > > >
> > > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > > >
> > > > > Hi,
> > > > > I’ve been building my cellbrowsers for matrix files for a while
> now
> > > and
> > > > > was working fine but after some update the pipeline doesn’t seem
> to
> > be
> > > > > working any more.
> > > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > > features.tsv.gz to the cellbrowser by first building the
> > > > exprMatrix.tsv.gz
> > > > > using “cbTool mtx2tsv …” and that step seem to work but then
next
> > step
> > > > > cbSeurat is failing.
> > > > > Any idea what can be the problem? Is it a problem of using
Seurat
> > > 5.0.0
> > > > w/
> > > > > latest version of cellbrowser?
> > > > > Thanks!
> > > > > Alejandro.
> > > > > ------------------------------
> > > > >
> > > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
> > > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > > INFO:root:Wrote R script to
> > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > INFO:root:running
> > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > through Rscript
> > > > > Seurat loaded, version 5.0.0
> > > > > [1] "Seurat: Reading data"
> > > > > [1] "Seurat: Reading data"
> > > > > [1] "Loading input data matrix"
> > > > > [1] "Loading tsv file with read.delim"
> > > > > [1] "Seurat: Setup"
> > > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
> min.genes
> > =
> > > > > 200) :
> > > > > argument "counts" is missing, with no default
> > > > > Execution halted
> > > > >
> > > > > real 1m33.191s
> > > > > user 1m17.847s
> > > > > sys 0m1.896s
> > > > > INFO:root:Wrote logfile of R run to
> > > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > > ERROR:root:R script did not complete successfully. Check
> > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > > analysisLog.txt.
> > > > >
> > > > > —
> > > > > Reply to this email directly, view it on GitHub
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OK, I installed the most current versions of everything, what I found in
conda and pip:
Python 3.9.5 (conda)
All others with pip --upgrade, so some more recent than yours:
Scipy 1.11.4
scanpy 1.9.6
numpy 1.26.2
and cbScanpy is working just fine on the pbmc3k dataset.
Your error message was this:
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6643, in cbScanpyCli
adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
figDir, logFname, skipMarkers)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 6432, in cbScanpy
adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
File "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
line 4651, in runSafeRankGenesGroups
clusterCellCounts =
list(adata.obs.groupby([clusterField]).apply(len).iteritems())
File "/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
line 6204, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'iteritems'
This looks like an installation problem with your pandas package. You can
try "pip install pandas --upgrade".
…On Mon, Dec 11, 2023 at 10:08 PM bugacov ***@***.***> wrote:
Hi….I was wondering if you were able to reproduce my errors? I think that
the main difference seems to be the Python version on my machine but I
kinda constrained to stay on that version if possible.
Let me know if there’s something else I can try.
Again the versions in my system are:
Python 3.9.18
scanpy==1.9.6
scipy==1.11.3
numpy==1.25.2
Thanks!
Alejandro.
From: Alejandro Bugacov ***@***.***>
Date: Tuesday, December 5, 2023 at 2:34 PM
To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
***@***.***>
Cc: Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
From: Maximilian Haeussler ***@***.***>
Reply-To: maximilianh/cellBrowser ***@***.***>
Date: Tuesday, December 5, 2023 at 7:23 AM
To: maximilianh/cellBrowser ***@***.***>
Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat: argument
"counts" is missing, with no default (Issue #265)
Ah, it's just that file. Yes, we do test and it works for me.
This looks a little like a problem with your scanpy installation... but
we'll see.
I'm using Python 3.7 and Scanpy 1.9.2 and scipy 1.7.3
I can try to use the same versions that you have. Can you send me the list
of these versions: Python, Scipy, Numpy and especially Scanpy.
Python 3.9.18
scanpy==1.9.6
scipy==1.11.3
numpy==1.25.2
Thanks!
Alejandro.
On Tue, Dec 5, 2023 at 4:11 PM bugacov ***@***.***> wrote:
> wget
> >
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=vfqy0VZ_lZZYeWdNabrBSDEqpde9StRJR_FA1l6CILg&e=>
> <
>
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=%3E
>
> > -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
> >
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=R827nUTL2RtYc_UutyP-51nWeHNYrD9Y0d0nnCisuhc&e=>
> ><
>
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=%3E
>
>
> Sent from my iPhone
>
> On Dec 5, 2023, at 1:15 AM, Maximilian Haeussler ***@***.***> wrote:
>
>
>
> Great, so this almost worked, it's only stuck at the markers calculation
> step at the end now. This should be easy to fix.
>
> You're using Python 3.9 from 2020 and combine that with the most recent
> scanpy version, just a few weeks old. We didn't test this combination.
You
> could downgrade scanpy to a few versions older. But yes, it should
> normally
> work, it's possible I have to add yet another workaround (I've kept
adding
> workarounds for the different scanpy versions, every few months,
something
> is breaking there).
>
> As soon as I can reproduce this error, I can fix it. Can you tell me
where
> you downloaded the mtx file from? Is this your own file or a 10X pbmc
demo
> file?
>
>
>
> On Tue, Dec 5, 2023 at 5:33 AM bugacov ***@***.***> wrote:
>
> > I actually uninstall cellbrowser and installed it again and now is
doing
> a
> > bit more but still throwing errors:
> >
> >
> > facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
> > cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> > pbmc3k
> > INFO:root:Loading Scanpy libraries
> > INFO:root:Creating scanpyOut
> > INFO:root:Loading Scanpy libraries
> > INFO:root:cbScanpy $Id$
> > INFO:root:Command: /usr/local/bin/cbScanpy -e
> > filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n pbmc3k
> > INFO:root:Matrix input file: filtered_gene_bc_matrices/hg19/matrix.mtx
> > INFO:root:Restricting OPENBLAS to 4 threads
> > INFO:root:Start time: 2023-12-05 04:30:26.199478
> > -----
> > anndata 0.10.3
> > scanpy 1.9.6
> > -----
> > PIL 10.0.0
> > asciitree NA
> > cellbrowser v1.2.3
> > cffi 1.14.5
> > colorama 0.4.4
> > cycler 0.12.1
> > cython_runtime NA
> > dateutil 2.8.2
> > entrypoints 0.4
> > exceptiongroup 1.2.0
> > fasteners 0.18
> > get_annotations NA
> > h5py 3.10.0
> > igraph 0.10.8
> > importlib_resources NA
> > joblib 1.3.2
> > kiwisolver 1.4.5
> > llvmlite 0.41.1
> > louvain 0.8.1
> > matplotlib 3.8.2
> > mpl_toolkits NA
> > natsort 8.4.0
> > numba 0.58.1
> > numcodecs 0.11.0
> > numpy 1.25.2
> > packaging 23.1
> > pandas 2.1.3
> > pkg_resources NA
> > psutil 5.8.0
> > pyparsing 3.1.1
> > pytz 2021.1
> > scipy 1.11.3
> > session_info 1.0.0
> > setuptools_scm NA
> > six 1.15.0
> > sklearn 1.3.2
> > texttable 1.7.0
> > threadpoolctl 3.2.0
> > typing_extensions NA
> > yaml 5.4.1
> > zarr 2.16.1
> > zipp NA
> > zoneinfo NA
> > -----
> > Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red
Hat
> > 11.4.1-2)]
> > Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> > -----
> > Session information updated at 2023-12-05 04:30
> > INFO:root:Loading Scanpy libraries
> > INFO:root:Loading expression matrix: mtx format
> > INFO:root:Data has 2700 samples/observations
> > INFO:root:Data has 32738 genes/variables
> > INFO:root:Basic filtering: keep only cells with min 200 genes
> > INFO:root:Basic filtering: keep only gene with min 3 cells
> > INFO:root:After filtering: Data has 2700 samples/observations and
13714
> > genes/variables
> > INFO:root:Making gene names unique
> > INFO:root:'geneIdType' is not specified in config file or set to
'auto'.
> > INFO:root:Auto-detected gene IDs type: symbols
> > INFO:root:Remove cells with more than 0.050000 percent of
mitochondrial
> > genes
> > INFO:root:Computing percentage of mitochondrial genes
> > WARNING: saving figure to file scanpyOut/figs/violin.png
> > INFO:root:Remove cells with less than 10 and more than 15000 genes
> > INFO:root:Keeping only cells with < 15000 genes
> > INFO:root:After filtering: Data has 2643 samples/observations and
13714
> > genes/variables
> > INFO:root:Keeping only cells with > 10 genes
> > INFO:root:After filtering: Data has 2643 samples/observations and
13714
> > genes/variables
> > INFO:root:Expression normalization, counts per cell = 10000
> > INFO:root:Did log2'ing of data
> > INFO:root:Finding highly variable genes
> > WARNING: saving figure to file
> scanpyOut/figs/filter_genes_dispersion.png
> > INFO:root:After high-var filtering: Data has 2643 samples/observations
> and
> > 1844 genes/variables
> > INFO:root:Regressing out percent_mito and number of UMIs
> > INFO:root:Scaling data, max_value=10
> > INFO:root:Performing initial PCA, number of PCs: 100
> > WARNING: saving figure to file scanpyOut/figs/pca_variance_ratio.png
> > INFO:root:Estimating number of useful PCs based on Shekar et al, Cell
> 2016
> > INFO:root:PC weight cutoff used is (sqrt(# of Genes/# of cells) + 1)^2
> > INFO:root:See http://www.cell.com/cell/fulltext/S0092-8674(16)31007-8
<<
https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=V7ZgmTdvAWsVTOnGdosk-ZKl0Rd7rUdm2Pt_Q236vTI&e=>
>
https://urldefense.us/v2/url?u=http-3A__www.cell.com_cell_fulltext_S0092-2D8674-2816-2931007-2D8&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=LRCerhXenZ3f2SWEPhr8kULBEGklU2NYVJ-O5nUQ-tA&e=%3E,
>
> > STAR methods
> > INFO:root:7 PCs will be used for tSNE and clustering
> > INFO:root:Performing tSNE
> > INFO:root:Running knn, using 7 PCs and 6 neighbors
> > INFO:root:Performing Louvain Clustering, resolution 1.000000
> > INFO:root:Found 13 louvain clusters
> > INFO:root:Using cluster annotation from field: louvain
> > WARNING: saving figure to file scanpyOut/figs/tsne.png
> > INFO:root:Performing UMAP
> > INFO:root:Performing Layout 'drl' = DrL Distributed Recursive Layout
> > INFO:root:Finding top markers for each cluster
> > INFO:root:Loading Scanpy libraries
> > Traceback (most recent call last):
> > File "/usr/local/bin/cbScanpy", line 8, in <module>
> > sys.exit(cbScanpyCli())
> > File
> "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> > line 6643, in cbScanpyCli
> > adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> > figDir, logFname, skipMarkers)
> > File
> "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> > line 6432, in cbScanpy
> > adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
> > File
> "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> > line 4651, in runSafeRankGenesGroups
> > clusterCellCounts =
> > list(adata.obs.groupby([clusterField]).apply(len).iteritems())
> > File
"/usr/local/lib64/python3.9/site-packages/pandas/core/generic.py",
> > line 6204, in __getattr__
> > return object.__getattribute__(self, name)
> > AttributeError: 'Series' object has no attribute 'iteritems'
> > facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData/data]
> >
> >
> >
> >
> >
> > From: Alejandro Bugacov ***@***.***>
> > Date: Monday, December 4, 2023 at 7:49 PM
> > To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> > ***@***.***>
> > Cc: Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Hi….I tried to run it on the example files from Scanpy example given
> here
> > https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html<<
https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html-253C&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=hkV8fjmu18Vu9JP99fI2Yr2oNegSCXgjEAuaMlSN-ps&e=>
>
https://urldefense.us/v2/url?u=https-3A__scanpy-2Dtutorials.readthedocs.io_en_latest_pbmc3k.html&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=fwTJ3jAfqNQubzg5eA4igcNVVQaoKw84DwvDYjI16tM&e=%3E
>
> >
> > wget
> >
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=vfqy0VZ_lZZYeWdNabrBSDEqpde9StRJR_FA1l6CILg&e=>
> <
>
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=sVd8NBPPExycR3HnZDVwe3_RsI7oJvmwWVUbzRPIScc&e=%3E
>
> > -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz<
> >
>
http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz%20-O%20data/pbmc3k_filtered_gene_bc_matrices.tar.gz
<
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Eqtc9jHwHZU0WqB7tfCK_xU-wHip2pNbZHBHzeETtRHMmpV-ntmbtudYUj4UyfoK&s=R827nUTL2RtYc_UutyP-51nWeHNYrD9Y0d0nnCisuhc&e=>
> ><
>
https://urldefense.us/v2/url?u=http-3A__cf.10xgenomics.com_samples_cell-2Dexp_1.1.0_pbmc3k_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-2520-2DO-2520data_pbmc3k-5Ffiltered-5Fgene-5Fbc-5Fmatrices.tar.gz-253E&d=DwQFaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=daN-itZmdDhtlnSO-ZKNiA&m=Qi2zRSMbkGew5N7ku4dNpPvlREN86rpFRZ7xEra3aLvTfppUj3r-CiybjUNGKzoV&s=hcBjGM9GQUNRZAiQBn_Kz8qAbb7sSHh-aBH5Suc5hMg&e=%3E
>
> >
> >
> > and I cannot get cbScanpy to run on them.
> >
> > I built the .h5ad file in python using
> >
> > import numpy as np
> > import pandas as pd
> > import scanpy as sc
> >
> > adata = sc.read_10x_mtx(
> > 'data/filtered_gene_bc_matrices/hg19/', # the directory with the
`.mtx`
> > file
> > var_names='gene_symbols', # use gene symbols for the variable names
> > (variables-axis index)
> > cache=True) # write a cache file for faster subsequent reading
> >
> > adata
> >
> >
> > and then tried to run the
> >
> > cbImportScanpy -i filtered_gene_bc_matrices-hg19-matrix.h5ad -o
> > pbmc3kImportScanpy
> >
> > But that give errors too.
> >
> > I
> >
> >
> > From: Alejandro Bugacov ***@***.***>
> > Date: Monday, December 4, 2023 at 11:36 AM
> > To: maximilianh/cellBrowser ***@***.***>, maximilianh/cellBrowser
> > ***@***.***>
> > Cc: Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > I’m not sure if I follow. Your example online points to a file
> >
> > cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o scanpyOut -n
> > pbmc3k
> >
> > But what you mean here is that I need to put all 3 files under a
folder
> > and use that name convention?
> > So I put all 3 files in a folder
> >
> > facebase-pipeline::root[/var/www/scratch/cellbrowser/cellData] ls -l
> > test1/
> > total 106608
> > -rw-r--r--. 1 root root 46082 Dec 4 19:17 barcodes.tsv.gz
> > -rw-r--r--. 1 root root 251118 Dec 4 19:17 features.tsv.gz
> > -rw-r--r--. 1 root root 108861485 Dec 4 18:51 matrix.mtx.gz
> >
> > And then tried passing the folder name but I get error like below
seems
> > like is looking for the h5ad file?
> >
> >
> >
> > cbScanpy -e test1 -o scanpyOut -n testOut
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:cbScanpy $Id$
> >
> > INFO:root:Command: /usr/local/bin/cbScanpy -e test1 -o scanpyOut -n
> > testOut
> >
> > INFO:root:Matrix input file: test1
> >
> > INFO:root:Restricting OPENBLAS to 4 threads
> >
> > INFO:root:Start time: 2023-12-04 19:31:04.112141
> >
> > -----
> >
> > anndata 0.10.3
> >
> > scanpy 1.9.6
> >
> > -----
> >
> > PIL 10.0.0
> >
> > asciitree NA
> >
> > cellbrowser v1.0.1
> >
> > cffi 1.14.5
> >
> > colorama 0.4.4
> >
> > cycler 0.12.1
> >
> > cython_runtime NA
> >
> > dateutil 2.8.2
> >
> > entrypoints 0.4
> >
> > exceptiongroup 1.2.0
> >
> > fasteners 0.18
> >
> > get_annotations NA
> >
> > h5py 3.10.0
> >
> > igraph 0.10.8
> >
> > importlib_resources NA
> >
> > joblib 1.3.2
> >
> > kiwisolver 1.4.5
> >
> > llvmlite 0.41.1
> >
> > louvain 0.8.1
> >
> > matplotlib 3.8.2
> >
> > mpl_toolkits NA
> >
> > natsort 8.4.0
> >
> > numba 0.58.1
> >
> > numcodecs 0.11.0
> >
> > numpy 1.25.2
> >
> > packaging 23.1
> >
> > pandas 2.1.3
> >
> > pkg_resources NA
> >
> > psutil 5.8.0
> >
> > pyparsing 3.1.1
> >
> > pytz 2021.1
> >
> > scipy 1.11.3
> >
> > session_info 1.0.0
> >
> > setuptools_scm NA
> >
> > six 1.15.0
> >
> > sklearn 1.3.2
> >
> > texttable 1.7.0
> >
> > threadpoolctl 3.2.0
> >
> > typing_extensions NA
> >
> > yaml 5.4.1
> >
> > zarr 2.16.1
> >
> > zipp NA
> >
> > zoneinfo NA
> >
> > -----
> >
> > Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red
Hat
> > 11.4.1-2)]
> >
> > Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> >
> > -----
> >
> > Session information updated at 2023-12-04 19:31
> >
> > INFO:root:Loading Scanpy libraries
> >
> > INFO:root:Loading expression matrix: mtx format
> >
> > Traceback (most recent call last):
> >
> > File "/usr/local/bin/cbScanpy", line 8, in <module>
> >
> > sys.exit(cbScanpyCli())
> >
> > File
> "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> > line 5865, in cbScanpyCli
> >
> > adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname,
> > figDir, logFname)
> >
> > File
> "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> > line 5407, in cbScanpy
> >
> > adata = readMatrixAnndata(matrixFname,
> > samplesOnRows=options.samplesOnRows, genome=options.genome)
> >
> > File
> "/usr/local/lib/python3.9/site-packages/cellbrowser/cellbrowser.py",
> > line 4803, in readMatrixAnndata
> >
> > adata = sc.read(matrixFname, cache=False).T
> >
> > File "/usr/local/lib/python3.9/site-packages/scanpy/readwrite.py",
line
> > 127, in read
> >
> > raise ValueError(
> >
> > ValueError: Reading with filekey 'test1' failed, the inferred filename
> > PosixPath('write/test1.h5ad') does not exist. If you intended to
provide
> a
> > filename, either use a filename ending on one of the available
> extensions
> > {'h5', 'anndata', 'txt', 'data', 'mtx.gz', 'tab', 'xlsx', 'tsv',
'h5ad',
> > 'csv', 'mtx', 'loom', 'soft.gz'} or pass the parameter `ext`.
> >
> >
> >
> >
> >
> >
> > From: Maximilian Haeussler ***@***.***>
> > Reply-To: maximilianh/cellBrowser ***@***.***>
> > Date: Monday, December 4, 2023 at 11:15 AM
> > To: maximilianh/cellBrowser ***@***.***>
> > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> argument
> > "counts" is missing, with no default (Issue #265)
> >
> > Yes, the error is because your filenames don't follow the usual
> > convention.
> > Can you rename your files to matrix.mtx.gz and features.tsv.gz and
> > barcodes.tsv.gz ? Or just create symlinks with this name. Then run it
> > again.
> >
> > I am not sure how/if I can solve this, this is a problem in scanpy, as
> it
> > only accepts the directory name, I think.
> >
> > On Mon, Dec 4, 2023 at 7:58 PM bugacov ***@***.***> wrote:
> >
> > > Hi….with the 2 mtx.gz files that I tried I did
> > >
> > >
> > >
> > > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> > >
> > >
> > >
> > > and get that need to specify a dir and not the mtx file for
> > > cellranger3-style .mtx
> > >
> > > I tried passing the name of a folder w/ the files but didn’t work
> > either.
> > >
> > > Can these mtx files be ran by with scanpy?
> > >
> > > Thanks,
> > >
> > > Alejandro.
> > >
> > > --------------------------
> > >
> > >
> > >
> > > cbScanpy -e bates_matrix.mtx.gz -o scanpyOut -n test1
> > >
> > > INFO:root:Loading Scanpy libraries
> > >
> > > INFO:root:Loading Scanpy libraries
> > >
> > > INFO:root:cbScanpy $Id$
> > >
> > > INFO:root:Command: /usr/local/bin/cbScanpy -e bates_matrix.mtx.gz -o
> > > scanpyOut -n test1
> > >
> > > INFO:root:Matrix input file: bates_matrix.mtx.gz
> > >
> > > INFO:root:Restricting OPENBLAS to 4 threads
> > >
> > > INFO:root:Start time: 2023-12-04 18:52:21.201824
> > >
> > > -----
> > >
> > > anndata 0.10.3
> > >
> > > scanpy 1.9.6
> > >
> > > -----
> > >
> > > PIL 10.0.0
> > >
> > > asciitree NA
> > >
> > > cellbrowser v1.0.1
> > >
> > > cffi 1.14.5
> > >
> > > colorama 0.4.4
> > >
> > > cycler 0.12.1
> > >
> > > cython_runtime NA
> > >
> > > dateutil 2.8.2
> > >
> > > entrypoints 0.4
> > >
> > > exceptiongroup 1.2.0
> > >
> > > fasteners 0.18
> > >
> > > get_annotations NA
> > >
> > > h5py 3.10.0
> > >
> > > igraph 0.10.8
> > >
> > > importlib_resources NA
> > >
> > > joblib 1.3.2
> > >
> > > kiwisolver 1.4.5
> > >
> > > llvmlite 0.41.1
> > >
> > > louvain 0.8.1
> > >
> > > matplotlib 3.8.2
> > >
> > > mpl_toolkits NA
> > >
> > > natsort 8.4.0
> > >
> > > numba 0.58.1
> > >
> > > numcodecs 0.11.0
> > >
> > > numpy 1.25.2
> > >
> > > packaging 23.1
> > >
> > > pandas 2.1.3
> > >
> > > pkg_resources NA
> > >
> > > psutil 5.8.0
> > >
> > > pyparsing 3.1.1
> > >
> > > pytz 2021.1
> > >
> > > scipy 1.11.3
> > >
> > > session_info 1.0.0
> > >
> > > setuptools_scm NA
> > >
> > > six 1.15.0
> > >
> > > sklearn 1.3.2
> > >
> > > texttable 1.7.0
> > >
> > > threadpoolctl 3.2.0
> > >
> > > typing_extensions NA
> > >
> > > yaml 5.4.1
> > >
> > > zarr 2.16.1
> > >
> > > zipp NA
> > >
> > > zoneinfo NA
> > >
> > > -----
> > >
> > > Python 3.9.18 (main, Sep 7 2023, 00:00:00) [GCC 11.4.1 20230605 (Red
> Hat
> > > 11.4.1-2)]
> > >
> > > Linux-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
> > >
> > > -----
> > >
> > > Session information updated at 2023-12-04 18:52
> > >
> > > INFO:root:Loading Scanpy libraries
> > >
> > > ERROR:root:For cellranger3-style .mtx files, please specify the
> > directory,
> > > not the .mtx.gz file name
> > >
> > >
> > > From: Maximilian Haeussler ***@***.***>
> > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > Date: Friday, December 1, 2023 at 12:03 PM
> > > To: maximilianh/cellBrowser ***@***.***>
> > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > argument
> > > "counts" is missing, with no default (Issue #265)
> > >
> > > Yes try cbScanpy ! It does exactly that !
> > >
> > > On Fri, Dec 1, 2023 at 19:01 bugacov ***@***.***> wrote:
> > >
> > > > Hi…Thanks again for your response. I’m trying to setup a somehow
> > generic
> > > > process where I take a set of matrix.mtx, features.tsv and
> > barcodes.tsv
> > > > files and visualize them w/ the cellbrowser.
> > > > I’m not sure if that contains the UMAP coords and clustering or of
> > they
> > > > always will so that’s why I thought I had to go thru’ Seurat but
if
> > not
> > > > needed and you can point me to an example on how to go directly to
> the
> > > > cellbrowser I’d really appreciate.
> > > >
> > > > In the meantime I’ll try to see if I can get the cbScanpy to work
w/
> > > these
> > > > files!
> > > > Thanks!
> > > > Alejandro.
> > > >
> > > >
> > > > From: Maximilian Haeussler ***@***.***>
> > > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > > Date: Friday, December 1, 2023 at 6:53 AM
> > > > To: maximilianh/cellBrowser ***@***.***>
> > > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running cbSeurat:
> > > argument
> > > > "counts" is missing, with no default (Issue #265)
> > > >
> > > > Wait... why are you running Seurat? you're running cbSeurat, Sorry
I
> > > > didn't see that, I was convinced that you're using cbImportSeurat.
> > > >
> > > > I haven't tested cbSeurat in a long time! I should probably retire
> it.
> > > >
> > > > Don't you have umap coordinates etc as tsv files? If so, you can
go
> > > > directly to cbBuild.
> > > >
> > > > If you need UMAP coords and clustering and cluster markers, and
> these
> > > > things are not already there in the meta or separate tsv files,
you
> > can
> > > > also use cbScanpy, which at this point has had a ton more testing.
> > > >
> > > > On Thu, Nov 30, 2023 at 10:35 PM bugacov ***@***.***> wrote:
> > > >
> > > > > Hi….The problem is that I’m having a lot of errors when trying
to
> > > > install
> > > > > Seurat 3 or 4. I was able to do it before but seem like it’s
> failing
> > > > now.
> > > > > Question: Is there a way of going from the matrix.mtx,
> features.tsv
> > > and
> > > > > barcodes.tsv directly into the cellbrowser w/o converting to
> Seurat?
> > > > >
> > > > > Thanks!
> > > > > Alejandro.
> > > > >
> > > > > From: Maximilian Haeussler ***@***.***>
> > > > > Reply-To: maximilianh/cellBrowser ***@***.***>
> > > > > Date: Thursday, November 30, 2023 at 11:59 AM
> > > > > To: maximilianh/cellBrowser ***@***.***>
> > > > > Cc: Alejandro Bugacov ***@***.***>, Author ***@***.***>
> > > > > Subject: Re: [maximilianh/cellBrowser] Issue w/ running
cbSeurat:
> > > > argument
> > > > > "counts" is missing, with no default (Issue #265)
> > > > >
> > > > > Hm yes I don’t think I’ve tested on Seurat. Do you want share
your
> > > > matrix
> > > > > ?
> > > > > Probably I’ll need to install Seurat5. Can you try it on Seurat
3
> or
> > 4
> > > ?
> > > > >
> > > > > On Thu, Nov 30, 2023 at 19:37 bugacov ***@***.***> wrote:
> > > > >
> > > > > > Hi,
> > > > > > I’ve been building my cellbrowsers for matrix files for a
while
> > now
> > > > and
> > > > > > was working fine but after some update the pipeline doesn’t
seem
> > to
> > > be
> > > > > > working any more.
> > > > > > I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and
> > > > > > features.tsv.gz to the cellbrowser by first building the
> > > > > exprMatrix.tsv.gz
> > > > > > using “cbTool mtx2tsv …” and that step seem to work but then
> next
> > > step
> > > > > > cbSeurat is failing.
> > > > > > Any idea what can be the problem? Is it a problem of using
> Seurat
> > > > 5.0.0
> > > > > w/
> > > > > > latest version of cellbrowser?
> > > > > > Thanks!
> > > > > > Alejandro.
> > > > > > ------------------------------
> > > > > >
> > > > > > cbSeurat --exprMatrix=exprMatrix.tsv.gz
> > > > > > --outDir=/var/www/scratch/cellbrowser/seurat_temp
--name=1W-YOON
> > > > > > INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
> > > > > > INFO:root:Wrote R script to
> > > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > > INFO:root:running
> > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
> > > > > > through Rscript
> > > > > > Seurat loaded, version 5.0.0
> > > > > > [1] "Seurat: Reading data"
> > > > > > [1] "Seurat: Reading data"
> > > > > > [1] "Loading input data matrix"
> > > > > > [1] "Loading tsv file with read.delim"
> > > > > > [1] "Seurat: Setup"
> > > > > > Error in CreateSeuratObject(raw.data = mat, min.cells = 3,
> > min.genes
> > > =
> > > > > > 200) :
> > > > > > argument "counts" is missing, with no default
> > > > > > Execution halted
> > > > > >
> > > > > > real 1m33.191s
> > > > > > user 1m17.847s
> > > > > > sys 0m1.896s
> > > > > > INFO:root:Wrote logfile of R run to
> > > > > > /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
> > > > > > ERROR:root:R script did not complete successfully. Check
> > > > > > /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and
> > > > > analysisLog.txt.
> > > > > >
> > > > > > —
> > > > > > Reply to this email directly, view it on GitHub
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#265 (comment)
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#265 (comment)
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Hi,
I’ve been building my cellbrowsers for matrix files for a while now and was working fine but after some update the pipeline doesn’t seem to be working any more.
I’m trying to go from the matrix.mtx.gz barcodes.tsv.gz and features.tsv.gz to the cellbrowser by first building the exprMatrix.tsv.gz using “cbTool mtx2tsv …” and that step seem to work but then next step cbSeurat is failing.
Any idea what can be the problem? Is it a problem of using Seurat 5.0.0 w/ latest version of cellbrowser?
Thanks!
Alejandro.
cbSeurat --exprMatrix=exprMatrix.tsv.gz --outDir=/var/www/scratch/cellbrowser/seurat_temp --name=1W-YOON
INFO:root:Creating /var/www/scratch/cellbrowser/seurat_temp
INFO:root:Wrote R script to /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R
INFO:root:running /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R through Rscript
Seurat loaded, version 5.0.0
[1] "Seurat: Reading data"
[1] "Seurat: Reading data"
[1] "Loading input data matrix"
[1] "Loading tsv file with read.delim"
[1] "Seurat: Setup"
Error in CreateSeuratObject(raw.data = mat, min.cells = 3, min.genes = 200) :
argument "counts" is missing, with no default
Execution halted
real 1m33.191s
user 1m17.847s
sys 0m1.896s
INFO:root:Wrote logfile of R run to /var/www/scratch/cellbrowser/seurat_temp/analysisLog.txt
ERROR:root:R script did not complete successfully. Check /var/www/scratch/cellbrowser/seurat_temp/runSeurat.R and analysisLog.txt.
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