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Issue with BayesPrism Gateway #72

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soph1azhao opened this issue Dec 16, 2023 · 1 comment
Open

Issue with BayesPrism Gateway #72

soph1azhao opened this issue Dec 16, 2023 · 1 comment

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@soph1azhao
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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/#) 
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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
@tinyi
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tinyi commented Dec 17, 2023 via email

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@tinyi @soph1azhao