'NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1)'

[ZabalaAitor]

Description of the bug

Hi!

I am getting an error during NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1):

ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1)'

Caused by:
  Process `NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1)` terminated with an error exit status (1)


Command executed [/home/azabala/.nextflow/assets/nf-core/circRNA/./workflows/circrna/../../subworkflows/local/../../modules/local/compute_correlations/templates/compute_correlations.R]:

  #!/usr/bin/env Rscript
  
  library(fishpond)
  suppressMessages(library(SummarizedExperiment))
  
  tx_expression <- readRDS('experiments.merged.rds')
  mi_expression <- read.table('mirna.normalized_counts_filtered.tsv', header=TRUE, row.names=1, sep='\t')
  interactions <- read.table('mirna.targets.1.tsv', sep='\t')
  
  tx_expression <- scaleInfReps(tx_expression)
  tx_expression <- labelKeep(tx_expression) # Here one can perform custom filtering
  
  if (!any(mcols(tx_expression)$keep)) {
      stop('No transcripts left after filtering')
  }
  
  result_cols <- c('stat', 'log2FC', 'pvalue', 'locfdr', 'qvalue')
  
  # Iterate rows of interactions
  for (i in 1:nrow(interactions)) {
      # Get miRNA and target gene
      miRNA <- interactions[i, 1]
      targets <- unlist(strsplit(interactions[i, 2], ','))
  
      mirna_expression <- mi_expression[miRNA,]
      transcript_expression <- tx_expression[targets,]
  
      if (!any(mcols(transcript_expression)$keep)) {
          print(paste('No transcripts left after filtering for miRNA', miRNA))
          next
      }
  
      # Add miRNA expression to colData so that it can be used for correlation
      colData(transcript_expression) <- cbind(
          colData(transcript_expression),
          t(mirna_expression[, rownames(colData(transcript_expression))])
      )
  
      result <- rowData(swish(transcript_expression, miRNA, cor = "pearson"))[, result_cols]
      result <- result[complete.cases(result), ]
      write.table(result, paste0(miRNA, '.tsv'), sep = '\t')
  }
  
  ################################################
  ################################################
  ## VERSIONS FILE                              ##
  ################################################
  ################################################
  
  r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
  
  writeLines(
      c(
          '"NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS":',
          paste('    r-base:', r.version)
      ),
  'versions.yml')
  
  ################################################
  ################################################
  ################################################
  ################################################

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 't': undefined columns selected
  Calls: cbind ... standardGeneric -> eval -> eval -> eval -> t -> [ -> [.data.frame
  Execution halted

Work dir:
  /scratch/azabala/network/circRNA/work_circRNA/fb/8cd9537a6b1538f793cd1c4367e95d

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

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Command used and terminal output

#!/bin/bash
#SBATCH --partition=biogipuzkoa-exclusive
#SBATCH --account=biogipuzkoa-exclusive
#SBATCH --time=700-00:00:00
#SBATCH --nodes=1              
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --mem=450GB
#SBATCH --mail-user=aitor.zabalagarcia@bio-gipuzkoa.eus
#SBATCH --mail-type=ALL
#SBATCH --err=/scratch/azabala/network/circRNA/errs/err
#SBATCH --out=/scratch/azabala/network/circRNA/outs/out_%j

module load Nextflow/24.04.2
module load Apptainer
module load Java
module load Miniforge3

nextflow pull nf-core/circrna

nextflow run nf-core/circRNA \
	-r  dev \
	-profile apptainer \
	--input /data/azabala/NIM_036/samplesheet_circRNA.csv \
	--phenotype /data/azabala/NIM_036/phenotype.csv \
	--outdir /scratch/azabala/network/circRNA \
	--tools 'ciriquant,circexplorer2,circrna_finder' \
    --bsj_reads 2 \
    --min_tools 2 \
	-w /scratch/azabala/network/circRNA/work_circRNA \
	--genome GRCh38 \
	--limitSjdbInsertNsj 3282245 \
	--mature /data/azabala/database/mature.fa \
    --mirna_expression /scratch/azabala/network/smallRNAseq/edger/mature_counts_fixed.tsv \
	--mirna_tools "miranda,targetscan" \
	--mirna_min_tools 1 \
	-c /scratch/azabala/network/custom.config \
	-resume

Relevant files

Nextflow version: 25.04.6
Hardware: HPC
Executor: slurm
Container: Apptainer
nf-core/circrna: dev

System information

No response