David Shechter
06/07/2024, 4:12 PMall(samples$sample_id %in% colnames(counts)) is not TRUE), but everything appears to be named and referenced correctly in my contrasts and samplesheet:
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 samplesheet_rnasplice.csv \
4 \
2 \
2 \
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: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Converting SIF file to temporary sandbox...
WARNING: Skipping mount /gs/gsfs0/home/dshecht1/.conda/envs/nfcore/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) :
all(samples$sample_id %in% colnames(counts)) is not TRUE
Calls: <Anonymous> -> stopifnot
Execution halted
INFO: Cleaning up image...