rnasplice
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STAGER error: subscript out of bounds
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: 9fe10b01e3 [dev]
Debian 10