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Hello everyone, Thanks to the nf-core community f...
# rnasplice
s
Hello everyone, Thanks to the nf-core community for putting together the rnasplice pipeline. I’ve just tried the pipeline but unfortunately after several hours it terminated with an error message. The error message is below. Does anybody have an idea what may have gone wrong (sorry for my ignorance, but I could not debug the issue myself.) I can provide further details if needed. Many thanks, Steven 
Run Name: angry_ptolemy
 
Execution completed unsuccessfully!
 
The exit status of the task that caused the workflow execution to fail was: 0.
The full error message was:
Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (KO_180-WT_180)'
Caused by:
`Missing output file(s) 
*.clustvec
expected by process `NFCORE_RNASPLICERNASPLICESUPPA_SALMON:CLUSTEREVENTS_IOI (KO_180-WT_180)`` 
Command executed:
suppa.py \
clusterEvents \
--dpsi KO_180-WT_180_transcript_diffsplice.dpsi \
--psivec KO_180-WT_180_transcript_diffsplice.psivec \
--dpsi-threshold 0.05 \
--eps 0.05 \
--metric euclidean \
--min-pts 20 \
--groups 1-3,4-6 \
--clustering DBSCAN \
-o KO_180-WT_180_transcript_cluster
cat -END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI":
suppa: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('suppa').version)")
END_VERSIONS
Command exit status:
0
Command output:
Number of clustered events: 114/624 (18.269231%)
Cluster 0 contains 71 events
Cluster 1 contains 43 events
The RMSSTD score for cluster 0 is 0.283342
The RMSSTD score for cluster 1 is 0.266318
The average silhouette score is : 0.755640
Command error:
INFO:   Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred
INFO:   Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO:   Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:   Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
Work dir:
/scratch/swingett/test_run_rnasplice/work/33/5d3fee492a0b37137d93458dc894f9
Container:
/public/singularity/containers/nextflow/depot.galaxyproject.org-singularity-suppa-2.3--py36_0.img
Tip: when you have fixed the problem you can continue the execution adding the option
-resume` to the run command line` 
The command used to launch the workflow was as follows:
nextflow run nf-core/rnasplice -r 1.0.4 --input YB_RNA_datasheet.csv --contrasts YB_RNA_contrast.csv --genome homo_sapiens.GRCh38.release_102 -config /public/singularity/containers/nextflow/lmb-nextflow/lmb.config --outdir results_rnasplice -bg
Execution summary
 
Launch time
26-Jan-2026 10:22:33
Ending time
26-Jan-2026 19:49:47 (duration: 9h 27m 14s)
Total CPU-Hours
577.4 (0% failed)
Tasks stats
Succeeded: 88  Cached: 0  Ignored: 0  Failed: 4
Launch directory
/scratch/swingett/test_run_rnasplice
Work directory
/scratch/swingett/test_run_rnasplice/work
Project directory
/lmb/home/swingett/.nextflow/assets/nf-core/rnasplice
Script name
<http://main.nf|main.nf>
Script ID
93d808d3e7ec52e0026e14613cc4d4c9
Workflow session
f077060d-c424-428a-bd16-3043f97b0147
Workflow repo
<https://github.com/nf-core/rnasplice>
Workflow revision
1.0.4 (1d0494ae3402d1a46e0adadad24f81a0ff855c77)
Workflow profile
standard
Workflow container
-
Container engine
singularity
Wave enabled
false
Fusion enabled
false, version -
Nextflow version
25.10.3, build 10983 (22-01-2026 15:34 UTC)
t
It apparently can't find some file(s) that should been produced, specifically 
*.clustvec
. I would go to 
/scratch/swingett/test_run_rnasplice/work/33/5d3fee492a0b37137d93458dc894f9
(the work dir of the process) and see what files are there. I would also look at the 
.command.{err,out,log}
files there to see if there are any messages to explain what went wrong, causing the missing files. (I don't recall encountering this, so the best I can do is give tips for debugging.) Pro tip: Typing ````` (or 
Ctrl-Alt-Shift-c
) gives you a window for pasting terminal output, messages, code, etc.
s
Hi, Thanks very much for getting back to me. I’ve looked into this some more and I think the reason for those file being missing is the results of an earlier process failing – specifically I think the sorting of the bam file runs out of RAM. I’ve tried to edit the config file to allocate more memory to SAMTOOLS_SORT. However, I’ve just realised that the config file does not seem to be recognised by nextflow. My input command is:
Copy code
nextflow run nf-core/rnasplice -r 1.0.4 --input YB_RNA_datasheet.csv --contrasts YB_RNA_contrast.csv --genome homo_sapiens.GRCh38.release_102 -config /public/singularity/containers/nextflow/lmb-nextflow/lmb.config --outdir results_rnasplice -bg
But the config file lmb.config appears not to have been recognised by Nextflow:
Copy code
nf-core/rnasplice v1.0.4-g1d0494a
------------------------------------------------------
Core Nextflow options
  revision                  : 1.0.4
  runName                   : big_wescoff
  containerEngine           : singularity
  launchDir                 : /scratch/swingett/test_run_rnasplice
  workDir                   : /scratch/swingett/test_run_rnasplice/work
  projectDir                : /lmb/home/swingett/.nextflow/assets/nf-core/rnasplice
  userName                  : swingett
  profile                   : standard
  configFiles               : 

Input/output options
Do you know why the config file is not recognised? Many thanks, Steven
t
I think the config file might be recognized, the 
configFiles
field just doesn't show it (this is normal, I don't know what that field is for). In your 
.nextflow.log
, look for lines with 
nextflow.config.ConfigBuilder - User config file:
-- that should show your file.
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