Description
Description of the bug
I'm getting an error with DRIMSeq when I try to run rnasplice. The pipeline works fine with other samples, so I'm not sure what's causing this error.
Command used and terminal output
Command Used:
nextflow run nf-core/rnasplice -profile docker -params-file /path/to/params.yaml
Error message:
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1)
Command executed:
run_drimseq_filter.R salmon.merged.txi.dtu.rds tximport.tx2gene.tsv Arc_RIPseq-samplesheet.csv \
6 \
3 \
3 \
10 \
0.1 \
10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-drimseq: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) :
all(samples$sample_id %in% colnames(counts)) is not TRUE
Calls: <Anonymous> -> stopifnot
Execution haltedRelevant files
Samplesheet file:
sample,fastq_1,fastq_2,strandedness,condition
ID11-IP-Arc-R2,/path/to/rawdata/ID11-IP-Arc-R2_1.fastq.gz,/path/to/rawdata/ID11-IP-Arc-R2_2.fastq.gz,unstranded,treatment
IP-Arc-R1,/path/to/rawdata/IP-Arc-R1_1.fastq.gz,/path/to/rawdata/IP-Arc-R1_2.fastq.gz,unstranded,treatment
ID-2-Arc-IP-R3,/path/to/rawdata/ID-2-Arc-IP-R3_1.fastq.gz,/path/to/rawdata/ID-2-Arc-IP-R3_2.fastq.gz,unstranded,treatment
ID-5-Non-IP-R3,/path/to/rawdata/ID-5-Non-IP-R3_1.fastq.gz,/path/to/rawdata/ID-5-Non-IP-R3_2.fastq.gz,unstranded,Control
ID12-Non-Arc-R2,/path/to/rawdata/ID12-Non-Arc-R2_1.fastq.gz,/path/to/rawdata/ID12-Non-Arc-R2_2.fastq.gz,unstranded,Control
Non-Arc-R1,/path/to/rawdata/Non-Arc-R1_1.fastq.gz,/path/to/rawdata/Non-Arc-R1_2.fastq.gz,unstranded,Control
params.yaml file:
input: '/path/to/sequencing_data/Arc_RIPseq-samplesheet.csv'
contrasts: '/path/to/sequencing_data/Arc_RIPseq-contrastsheet.csv'
outdir: '/path/to/sequencing_data/'
fasta: '/home/gimena/reference_files/BDGP6.32_ensemble/Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa'
gtf: '/home/gimena/reference_files/GTF_files/fromEnsembl/Drosophila_melanogaster.BDGP6.32.106.gtf'
source: 'fastq'
aligner: 'star_salmon'
min_samps_gene_expr: 6
min_gene_expr: 10
min_samps_feature_expr: 3
min_feature_expr: 10
min_samps_feature_prop: 3
min_feature_prop: 0.1
sashimi_plot: true
fig_height: 20
fig_width: 20
miso_genes: FBgn0265487
skip_bigwig: false
dexseq_dtu: true
suppa: false
edger_exon: false
dexseq_exon: false
rmats: false
System information
Nextflow Version: version 23.10.0
Linux OS
Version of nf-core/rnasplice 1.0.1