Danko-Lab
Issue with BayesPrism Gateway
Hi! I am trying the pancreas dataset on the BayesPrism Gateway. The experiment could not run though because of the belowStandard-Error. (looks like the package is not loaded.) Would you mind letting me know what is wrong with the operation? Thanks a lot!
[ Workspace ](https://django.bayesprism.org/workspace/experiments/Clone_of_Clone_of_pancreas_t1_on_Dec_14%2C_2023_8%3A46_8a3f0d5a-1e6a-4285-be9b-701488e503bf/#)
[Dashboard](https://django.bayesprism.org/workspace/dashboard)
[Experiments](https://django.bayesprism.org/workspace/experiments)
[Projects](https://django.bayesprism.org/workspace/projects)
[Storage](https://django.bayesprism.org/workspace/storage)
Experiment Summary
Standard-Error
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 241 100 120 100 121 2000 2016 --:--:-- --:--:-- --:--:-- 4016
Loading required package: BayesPrism
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'BayesPrism'
Error in plot.cor.phi(input = t(matRef), input.labels = cell.state.labels, :
could not find function "plot.cor.phi"
Error in plot.cor.phi(input = t(matRef), input.labels = cell.type.labels, :
could not find function "plot.cor.phi"
Error in plot.scRNA.outlier(input = t(matRef), cell.type.labels = cell.type.labels, :
could not find function "plot.scRNA.outlier"
Error in plot.bulk.outlier(bulk.input = t(matX), sc.input = t(matRef), :
could not find function "plot.bulk.outlier"
Error in cleanup.genes(i
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 241 100 120 100 121 2000 2016 --:--:-- --:--:-- --:--:-- 4016
Loading required package: BayesPrism
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'BayesPrism'
Error in plot.cor.phi(input = t(matRef), input.labels = cell.state.labels, :
could not find function "plot.cor.phi"
Error in plot.cor.phi(input = t(matRef), input.labels = cell.type.labels, :
could not find function "plot.cor.phi"
Error in plot.scRNA.outlier(input = t(matRef), cell.type.labels = cell.type.labels, :
could not find function "plot.scRNA.outlier"
Error in plot.bulk.outlier(bulk.input = t(matX), sc.input = t(matRef), :
could not find function "plot.bulk.outlier"
Error in cleanup.genes(input = t(matRef), input.type = "count.matrix", :
could not find function "cleanup.genes"
Execution halted
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 243 100 120 100 123 1558 1597 --:--:-- --:--:-- --:--:-- 3155
The output of Standard-Out shows no special indication
Using: R --vanilla --slave --args 16 /ocean/projects/bio210011p/dreg2016/BayesPrism-gateway -x pancreas_bulk_v2.tsv -x.type tsv -ref pancreas_scref_v2.tsv -ref.file.type tsv -ref.data.type scRNA -file.cell.type pancreasref_cellprofile.csv -species hs -out out < /ocean/projects/bio210011p/dreg2016/BayesPrism-gateway/run_bayes.R
CPU cores: 16
Bulk count matrix: pancreas_bulk_v2.tsv
Bulk file type: tsv
Reference count matrix: pancreas_scref_v2.tsv
Reference file type: tsv
Reference data type: scrna
file of cell type: pancreasref_cellprofile.csv
Output prefix: out
Species: hs
1) -------- Load count matrix
[1] "[X matrix]\n"
int [1:25525, 1:7] 360 388 3679 118 1522 335 4046 1623 1922 664 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:25525] "SGIP1" "AZIN2" "CLIC4" "AGBL4" ...
..$ : chr [1:7] "HP1504101T2D_wholeislet" "HP1506401_wholeislet" "HP1504901_wholeislet" "HP1508501T2D_wholeislet" ...
NULL
HP1504101T2D_wholeislet HP1506401_wholeislet HP1504901_wholeislet HP1508501T2D_wholeislet HP1507101_wholeislet
SGIP1 360 616 204 567 171
AZIN2 388 344 434 405 729
CLIC4 3679 2753 4151 5125 3241
AGBL4 118 155 209 137 289
NECAP2 1522 1737 1562 2754 1870
SLC45A1 335 376 288 343 372
[1] "[Reference matrix]\n"
int [1:25525, 1:410] 0 0 3 0 0 0 0 55 4 0 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:25525] "SGIP1" "AZIN2" "CLIC4" "AGBL4" ...
..$ : chr [1:410] "delta" "alpha" "delta.1" "gamma" ...
NULL
delta alpha delta.1 gamma ductal
SGIP1 0 0 0 32 0
AZIN2 0 0 0 0 0
CLIC4 3 0 3 1 0
AGBL4 0 0 0 0 0
NECAP2 0 0 0 0 0
SLC45A1 0 0 0 0 0
[1] "[Cell type]\n"
'data.frame': 410 obs. of 4 variables:
$ cell_ID : chr "delta" "alpha" "delta.1" "gamma" ...
$ cell_type : chr "delta" "alpha" "delta" "gamma" ...
$ cell_subtype: chr "delta" "alpha" "delta-1" "gamma" ...
$ tumor_state : int 1 1 1 1 1 1 1 1 1 1 ...
NULL
cell_ID cell_type cell_subtype tumor_state
1 delta delta delta 1
2 alpha alpha alpha 1
3 delta.1 delta delta-1 1
4 gamma gamma gamma 1
5 ductal ductal ductal 1
6 alpha.1 alpha alpha-1 1
cell_ID cell_type cell_subtype tumor_state
1 delta delta delta 1
2 alpha alpha alpha 1
3 delta.1 delta delta-1 1
4 gamma gamma gamma 1
5 ductal ductal ductal 1
* Warning: 410 Cells in your reference matrix are used to proceed the next step.
./filefad76598e41c/
2) -------- Start bayesPrism
Dear user,
Thank you for reporting this issue. We have fixed it. Please try re-submitting your task.
Best,
Tinyi
On Sat, Dec 16, 2023 at 10:48 AM soph1azhao @.***> wrote:
Hi! I am trying the pancreas dataset on the BayesPrism Gateway https://django.bayesprism.org/. The experiment could not run though because of the belowStandard-Error. (looks like the package is not loaded.) Would you mind letting me know what is wrong with the operation? Thanks a lot!
Workspace Dashboard Experiments Projects Storage Experiment Summary Standard-Error % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 241 100 120 100 121 2000 2016 --:--:-- --:--:-- --:--:-- 4016 Loading required package: BayesPrism Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'BayesPrism' Error in plot.cor.phi(input = t(matRef), input.labels = cell.state.labels, : could not find function "plot.cor.phi" Error in plot.cor.phi(input = t(matRef), input.labels = cell.type.labels, : could not find function "plot.cor.phi" Error in plot.scRNA.outlier(input = t(matRef), cell.type.labels = cell.type.labels, : could not find function "plot.scRNA.outlier" Error in plot.bulk.outlier(bulk.input = t(matX), sc.input = t(matRef), : could not find function "plot.bulk.outlier" Error in cleanup.genes(i % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 241 100 120 100 121 2000 2016 --:--:-- --:--:-- --:--:-- 4016 Loading required package: BayesPrism Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'BayesPrism' Error in plot.cor.phi(input = t(matRef), input.labels = cell.state.labels, : could not find function "plot.cor.phi" Error in plot.cor.phi(input = t(matRef), input.labels = cell.type.labels, : could not find function "plot.cor.phi" Error in plot.scRNA.outlier(input = t(matRef), cell.type.labels = cell.type.labels, : could not find function "plot.scRNA.outlier" Error in plot.bulk.outlier(bulk.input = t(matX), sc.input = t(matRef), : could not find function "plot.bulk.outlier" Error in cleanup.genes(input = t(matRef), input.type = "count.matrix", : could not find function "cleanup.genes" Execution halted % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 243 100 120 100 123 1558 1597 --:--:-- --:--:-- --:--:-- 3155
The output of Standard-Out shows no special indication
Using: R --vanilla --slave --args 16 /ocean/projects/bio210011p/dreg2016/BayesPrism-gateway -x pancreas_bulk_v2.tsv -x.type tsv -ref pancreas_scref_v2.tsv -ref.file.type tsv -ref.data.type scRNA -file.cell.type pancreasref_cellprofile.csv -species hs -out out < /ocean/projects/bio210011p/dreg2016/BayesPrism-gateway/run_bayes.R CPU cores: 16 Bulk count matrix: pancreas_bulk_v2.tsv Bulk file type: tsv Reference count matrix: pancreas_scref_v2.tsv Reference file type: tsv Reference data type: scrna file of cell type: pancreasref_cellprofile.csv Output prefix: out Species: hs
- -------- Load count matrix [1] "[X matrix]\n" int [1:25525, 1:7] 360 388 3679 118 1522 335 4046 1623 1922 664 ...
- attr(*, "dimnames")=List of 2 ..$ : chr [1:25525] "SGIP1" "AZIN2" "CLIC4" "AGBL4" ... ..$ : chr [1:7] "HP1504101T2D_wholeislet" "HP1506401_wholeislet" "HP1504901_wholeislet" "HP1508501T2D_wholeislet" ... NULL HP1504101T2D_wholeislet HP1506401_wholeislet HP1504901_wholeislet HP1508501T2D_wholeislet HP1507101_wholeislet SGIP1 360 616 204 567 171 AZIN2 388 344 434 405 729 CLIC4 3679 2753 4151 5125 3241 AGBL4 118 155 209 137 289 NECAP2 1522 1737 1562 2754 1870 SLC45A1 335 376 288 343 372 [1] "[Reference matrix]\n" int [1:25525, 1:410] 0 0 3 0 0 0 0 55 4 0 ...
- attr(*, "dimnames")=List of 2 ..$ : chr [1:25525] "SGIP1" "AZIN2" "CLIC4" "AGBL4" ... ..$ : chr [1:410] "delta" "alpha" "delta.1" "gamma" ... NULL delta alpha delta.1 gamma ductal SGIP1 0 0 0 32 0 AZIN2 0 0 0 0 0 CLIC4 3 0 3 1 0 AGBL4 0 0 0 0 0 NECAP2 0 0 0 0 0 SLC45A1 0 0 0 0 0 [1] "[Cell type]\n" 'data.frame': 410 obs. of 4 variables: $ cell_ID : chr "delta" "alpha" "delta.1" "gamma" ... $ cell_type : chr "delta" "alpha" "delta" "gamma" ... $ cell_subtype: chr "delta" "alpha" "delta-1" "gamma" ... $ tumor_state : int 1 1 1 1 1 1 1 1 1 1 ... NULL cell_ID cell_type cell_subtype tumor_state 1 delta delta delta 1 2 alpha alpha alpha 1 3 delta.1 delta delta-1 1 4 gamma gamma gamma 1 5 ductal ductal ductal 1 6 alpha.1 alpha alpha-1 1 cell_ID cell_type cell_subtype tumor_state 1 delta delta delta 1 2 alpha alpha alpha 1 3 delta.1 delta delta-1 1 4 gamma gamma gamma 1 5 ductal ductal ductal 1
- Warning: 410 Cells in your reference matrix are used to proceed the next step. ./filefad76598e41c/
- -------- Start bayesPrism
— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/72, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS3ANXSU7VNWJCBF6QDYJUDYXAVCNFSM6AAAAABAXIHI3CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA2DINJXGU4DQNA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
