Description
Description of the bug
Hi there
Not sure why this error, happen, I have the idea that the genome give this file?
I have another question, regarding the MISO files, or Id, They can not find all the splicing??? why need to used ENSEMB, if I am using mm10, It will not work??
thank you
Command used and terminal output
N E X T F L O W ~ version 24.10.5
Launching `https://github.com/nf-core/rnasplice` [chaotic_galileo] DSL2 - revision: 1d0494ae34 [1.0.4]
genome : mm10
Max job request options
max_memory : 256.GB
Alignment options
save_align_intermeds : true
rMATS options
rmats : true
rmats_read_len : 90
DEXSeq DEU options
dexseq_exon : true
edgeR DEU options
edger_exon : true
DEXSeq DTU options
dexseq_dtu : true
min_samps_gene_expr : 4
min_samps_feature_expr: 2
min_samps_feature_prop: 2
Miso
sashimi_plot : true
miso_genes : null
miso_genes_file : nulRelevant files
No response
System information
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (genes.gtf)'
Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (genes.gtf) terminated with an error exit status (1)
Command executed:
dexseq_prepare_annotation.py genes.gtf DEXSeq.gff
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION":
htseq: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('htseq').version)")
dexseq_prepare_annotation.py", line 132, in
raise ValueError("Same name found on two strands: %s, %s" % (str(l[i]), str(l[i + 1])))
ValueError: Same name found on two strands: <GenomicFeature: exonic_part 'Gm4312+Gm4301' at chr10: 100366498 -> 100367412 (strand '+')>, <GenomicFeature: exonic_part 'Gm4312+Gm4301' at chr10: 100382559 -> 100381645 (strand '-')>