BiocParallel errors in rule AberrantExpression_pipeline_OUTRIDER_runOutrider_R about drop HOT 7 CLOSED

Hi, it seems the error is this:
Please provide for q an integer greater than 1 and smaller than number of samples or genes. That refers to the encoding dimension.
In your specific case it's due to your low number of samples (only 4 in GROUP1 and 3 in GROUP2). Are you attempting to do differential expression? If so, OUTRIDER is not the software you want.
For OUTRIDER to run, at least 10 samples are needed, although we recommend at least 50.

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Hi @gianfilippo - did you manage to resolve this error?

from drop.

Hi, I am back to this project again.
I downloaded a matrix of external counts to work around my small control sample size.
Not run yet, though, so I cannot say if this solves the problem

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UPDATE:
I tried to add a few external files, but I keep getting the error below. What am I doing wrong ?
config.yaml.txt
sampleTable.tsv.txt

======================================================
WARNING: 8 files missing in samples annotation. Ignoring...
WARNING: Less than 30 IDs in DROP_GROUP HC
WARNING: Less than 30 IDs in DROP_GROUP CR
WARNING: Less than 30 IDs in DROP_GROUP HC
WARNING: Less than 30 IDs in DROP_GROUP CR
$HOME/scripts/DROP/processed_data/aberrant_expression/params/config/AberrantExpression_config.tsv Param Files do not match. Updating to current Sample Annotation

$HOME/scripts/DROP/processed_data/aberrant_splicing/params/config/AberrantSplicing_config.tsv Param Files do not match. Updating to current Sample Annotation

check for missing R packages
install gagneurlab/FRASER
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16)
Installing github package(s) 'gagneurlab/FRASER'
Skipping install of 'FRASER' from a github remote, the SHA1 (9aaf97f1) has not changed since last install.
Use force = TRUE to force installation
installed gagneurlab/FRASER
MonoallelicExpression has been turned off in the config file
rnaVariantCalling has been turned off in the config file
Structuring dependencies...
Dependencies file generated at: /tmp/tmp57yf5e0p

Building DAG of jobs...
WorkflowError:
WorkflowError:
WorkflowError:
InputFunctionException (rule AberrantExpression_pipeline_Counting_mergeCounts_R, line 156, /tmp/tmp57yf5e0p):
Error:
KeyError: "Column 'GENE_ANNOTATION' not present in sample annotation."
Wildcards:
annotation=v41
dataset=HC
Traceback:
File "/tmp/tmp57yf5e0p", line 52, in
File "$HOME/.conda/envs/drop_env_133/lib/python3.8/site-packages/drop/config/submodules/AberrantExpression.py", line 61, in getCountFiles
File "$HOME/.conda/envs/drop_env_133/lib/python3.8/site-packages/drop/config/SampleAnnotation.py", line 276, in getImportCountFiles
File "$HOME/.conda/envs/drop_env_133/lib/python3.8/site-packages/drop/config/SampleAnnotation.py", line 183, in subsetSampleAnnotation
MissingInputException: Missing input files for rule markdown:
output: $HOME/scripts/DROP/html/AberrantExpression/Counting/v41/Summary_HC.html
wildcards: file=AberrantExpression/Counting/v41/Summary_HC
affected files:
AberrantExpression/Counting/v41/Summary_HC.md
MissingInputException: Missing input files for rule markdown:
output: $HOME/scripts/DROP/html/Scripts_AberrantExpression_pipeline_Counting_Datasets.html
wildcards: file=Scripts_AberrantExpression_pipeline_Counting_Datasets
affected files:
Scripts_AberrantExpression_pipeline_Counting_Datasets.md
MissingInputException: Missing input files for rule markdown:
output: $HOME/scripts/DROP/html/aberrant-expression-pipeline_index.html
wildcards: file=aberrant-expression-pipeline_index
affected files:
aberrant-expression-pipeline_index.md

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Hi, it seems that some of your DROP groups have less than 10 samples. What are you interested in comparing? All samples together? If so, they should all belong to the same group.

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Hi, I assigned all the samples to the same group, Healthy, and I still get the same error.

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Let me take it back. I found the mistake. I misspelled GENE_ANNOTATION in the sample annotation file. Sorry about this.
I do have a different error related to FRASER unable to load a shared object. I will make a separate report for this

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