Error in DGEList(counts = data, genes = rownames(data)) : non-numeric values found in counts

[mdozmorov]

Description of the bug

This issue is identical to #218, which was closed but not resolved. After debugging, the problem is that the data object being supplied to DGEList(counts=data,genes=rownames(data)) has 0 rows and 0 columns

smrnaseq/bin/edgeR_miRBase.r

Line 55 in 18d6c84

dataDGE<-DGEList(counts=data,genes=rownames(data))

The preceding code filters out rows and columns that have only zeros, but no code checks the data dimensions afterward.

This occurred when I analyzed two samples, to see if the pipeline runs. I'm new to Nextflow, don't know why my samples produce such results. Don't know how the output of edgeR_miRBase.r, or the lack of it, will affect the downstream steps.

Command used and terminal output

DIRIN=/Users/bluedot/data/WorkData/2023-08.miRNA-seq
INPUT=${DIRIN}/samplesheet_full.csv
DIROUT=${DIRIN}/OUT_test
GENOME=/Users/bluedot/data/ExtData/UCSC/hg38/hg38.fa
BWAINDEX=/Users/bluedot/data/ExtData/UCSC/hg38/hg38.fa
CHROMSIZE=/Users/bluedot/data/ExtData/UCSC/genometable.hg38.txt
MIRBASE_GFF=/Users/bluedot/data/ExtData/UCSC/hg38/hsa.gff3
MIRBASE_MATURE=/Users/bluedot/data/ExtData/UCSC/hg38/mature.fa
MIRBASE_HAIRPIN=/Users/bluedot/data/ExtData/UCSC/hg38/hairpin.fa

nextflow run nf-core/smrnaseq --input ${INPUT} \
  --outdir ${DIROUT} \
  -profile 'singularity' \
  --genome GRCh38 \
  --mirtrace_species 'hsa' \
  --protocol 'illumina' \
  --mirna_gtf ${MIRBASE_GFF} \
  --mature ${MIRBASE_MATURE} \
  --hairpin ${MIRBASE_HAIRPIN} \
  -resume
====

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC'

Caused by:
  Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC` terminated with an error exit status (1)

Command executed:

  edgeR_miRBase.r sample01_mature.sorted.idxstats sample09_mature.sorted.idxstats sample01_mature_hairpin.sorted.idxstats sample09_mature_hairpin.sorted.idxstats

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      limma: $(Rscript -e "library(limma); cat(as.character(packageVersion('limma')))")
      edgeR: $(Rscript -e "library(edgeR); cat(as.character(packageVersion('edgeR')))")
      data.table: $(Rscript -e "library(data.table); cat(as.character(packageVersion('data.table')))")
      gplots: $(Rscript -e "library(gplots); cat(as.character(packageVersion('gplots')))")
      methods: $(Rscript -e "library(methods); cat(as.character(packageVersion('methods')))")
      statmod: $(Rscript -e "library(statmod); cat(as.character(packageVersion('statmod')))")
  $hairpin
  [1] "sample01_mature_hairpin.sorted.idxstats"
  [2] "sample09_mature_hairpin.sorted.idxstats"

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred

  Attaching package: ‘gplots’

  The following object is masked from ‘package:stats’:

  $mature
  [1] "sample01_mature.sorted.idxstats"
  [2] "sample09_mature.sorted.idxstats"

  $hairpin
  [1] "sample01_mature_hairpin.sorted.idxstats"
  [2] "sample09_mature_hairpin.sorted.idxstats"

  Error in DGEList(counts = data, genes = rownames(data)) :
    non-numeric values found in counts
  Execution halted

Relevant files

No response

System information

nextflow version 23.04.1.5866
HPC
local
singularity
CentOS Linux 7
2.2.2

[mdozmorov]

The following helped me to complete the pipeline.

nextflow run nf-core/smrnaseq --input ${INPUT} \
  --outdir ${DIROUT} \
  -profile 'singularity' \
  --genome GRCh38 \
  --mirtrace_species 'hsa' \
  --protocol 'illumina' \
  --skip_mirdeep \
  -resume \
  -r fix-mirtop-gff

[christopher-mohr]

Hi @mdozmorov, can you confirm that this issue does not exist anymore in 2.3.0 ?

[atrigila]

I tried to reproduce this error in the latest dev version, using two samples as in the original post, but I couldn't. The pipeline completed successfully.

Code:

DIRIN=/workspace/
INPUT=${DIRIN}/smrnaseq/assets/samplesheet.csv
DIROUT=${DIRIN}/test_issue_282
// MIRBASE_GFF: This file is downloaded automatically if using iGenomes
// MIRBASE_MATURE: This file is downloaded automatically from mirbase if not provided
// MIRBASE_HAIRPIN: This file is downloaded automatically from mirbase if not provided

 nextflow run nf-core/smrnaseq \
--input ${INPUT}   \
--outdir ${DIROUT}   \
-profile illumina,singularity   \
--genome GRCh38   \
--mirtrace_species 'hsa'   \
-r dev 

Samplesheet:

sample,fastq_1
Clone1_N1,s3://ngi-igenomes/test-data/smrnaseq/C1-N1-R1_S4_L001_R1_001.fastq.gz
Clone9_N1,s3://ngi-igenomes/test-data/smrnaseq/C9-N1-R1_S7_L001_R1_001.fastq.gz