wf transcriptome differential analysis error in dmDSdata(counts = counts, samples = coldata)

[kjb141]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.4.0

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.1.14

CLI command run

epi2me-labs/wf-transcriptomes v1.4.0

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Error during pipeline:differential_expression:deAnalysis. Attempting to run wf transcriptome with differential expression analysis on data set of 16 samples (5 control, 10 treated). Keep getting error message of Error executing process > 'pipeline:differential_expression:deAnalysis (1)'

Relevant log output

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'pipeline:differential_expression:deAnalysis (1)'

Caused by:
  Process `pipeline:differential_expression:deAnalysis (1)` terminated with an error exit status (1)

Command executed:

  mkdir merged
  mkdir de_analysis
  de_analysis.R annotation.gtf 3 1 10 3 "sample_sheet.csv"

Command exit status:
  1

Command output:
  Loading counts, conditions and parameters.
  Checking annotation file type.
  Annotation file type is gtf.
  Checking annotation file for presence of transcript_id versions.
  Annotation file transcript_ids include versions.
  Loading annotation database.
  Filtering counts using DRIMSeq.

Command error:
  Warning message:
  package 'DRIMSeq' was built under R version 4.3.2 
  Warning messages:
  1: package 'GenomicFeatures' was built under R version 4.3.2 
  2: package 'BiocGenerics' was built under R version 4.3.2 
  3: package 'S4Vectors' was built under R version 4.3.3 
  4: package 'IRanges' was built under R version 4.3.3 
  5: package 'GenomeInfoDb' was built under R version 4.3.2 
  6: package 'GenomicRanges' was built under R version 4.3.3 
  7: package 'AnnotationDbi' was built under R version 4.3.2 
  8: package 'Biobase' was built under R version 4.3.3 
  Warning messages:
  1: package 'edgeR' was built under R version 4.3.3 
  2: package 'limma' was built under R version 4.3.3 
  Loading counts, conditions and parameters.
  Checking annotation file type.
  Annotation file type is gtf.
  Checking annotation file for presence of transcript_id versions.
  Annotation file transcript_ids include versions.
  Loading annotation database.
  Import genomic features from the file as a GRanges object ... OK
  Prepare the 'metadata' data frame ... OK
  Make the TxDb object ... OK
  Warning message:
  In .get_cds_IDX(mcols0$type, mcols0$phase) :
    The "phase" metadata column contains non-NA values for features of type
    stop_codon. This information was ignored.
  'select()' returned 1:many mapping between keys and columns
  Filtering counts using DRIMSeq.
  Error in dmDSdata(counts = counts, samples = coldata) : 
    mode(counts) %in% "numeric" is not TRUE
  Calls: dmDSdata -> stopifnot
  Execution halted

Work dir:
  /home/nic/epi2melabs/instances/wf-transcriptomes_01J9PGNNJK2WPEFKTNWQJ9Y6CY/work/01/be2af63026977e03c014820cacbedf

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[sarahjeeeze]

Hey, would you mind sharing your sample sheet

[sarahjeeeze]

Hey, dont forget to share the sample sheet

[kjb141]

Sorry, seems like it didn't upload properly. Here is the sample sheet:
sample_sheet.csv

[KatrinMoller]

I just ran into the same problem, this is my current sample sheet:
sample_sheet1.csv

[sigusn]

update. The issue with the sample sheet was that sample names contained hyphen "sample-1" instead of underscore "sample_1" this caused error in the DE step of the workflow.