STAGER error: subscript out of bounds

[paolo-kunderfranco]

Description of the bug

As referenced here #83

I am still stopped at this point:

run_stager.R CP_TG-CP_WT DEXSeqResults.CP_TG-CP_WT.tsv perGeneQValue.CP_TG-CP_WT.tsv dexseq

Error in[<-(tmp, idCon, 1, value = unlist(txLevelAdjustments)) : subscript out of bounds Calls: stageWiseAdjustment -> stageWiseAdjustment -> .local -> .stageWiseTest Execution halted

Any suggestion?
Best

Command used and terminal output

nextflow run nf-core/rnasplice --input $wd/samplesheet_orig.csv \
						--contrasts $wd/contrast.csv \
						--outdir splice_Brain_TG_vs_Brain_WT \
						--genome GRCm38 \
						--aligner star_salmon \
							--dexseq_exon true \
							--min_samps_gene_expr 2 \
							--min_samps_feature_expr 2 \
							--min_gene_expr 5 \
							   --min_feature_expr 5 \
							   --min_feature_prop 0.2 \
							   --edger_exon true\
							   --rmats false \
							   --dexseq_dtu true \
							   --suppa true \
							   --suppa_per_local_event true \
							   --suppa_per_isoform true \
							   --save_reference true \
							   --sashimi_plot false \
							   -config $wd/config_HPC.config \
							   -profile docker \
							   -r dev

Relevant files

contrast.csv
nextflow.log
splicing_P107535352.log

System information

N E X T F L O W ~ version 23.04.2
Launching https://github.com/nf-core/rnasplice [hopeful_gilbert] DSL2 - revision: 9fe10b0 [dev]
Debian 10

[jma1991]

Hello @paolo-kunderfranco

Please could you send the input files which are passed to the run_stage.R script where the error occurs. With the input files, we can run the script by hand and de-bug why the error has occurred.

Thank you,
James

[paolo-kunderfranco]

Archivio.zip

[paolo-kunderfranco]

no news?
Up to now I add --dexseq_dtu false to terminate the workflow

[jma1991]

Hello @paolo-kunderfranco

After some investigation, it seems the error is not specific to the pipeline or its operation but the underlying stageR package. I have opened an issue with the original developer here to see if we can work together to address the issue.

Thanks,
James