Comments (4)
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
from rnasplice.
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
from rnasplice.
from rnasplice.
no news?
Up to now I add --dexseq_dtu false
to terminate the workflow
from rnasplice.
Related Issues (20)
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The processes for splitting files are running very slowly with large numbers of input samples HOT 5
- Error: suppa_split_file.R Input_file must contain samplesheet samples. HOT 2
- ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)' HOT 11
- Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) HOT 3
- Error single-end execution HOT 1
- Error in SUPPA: Clustergroups are assigned incorrectly HOT 4
- Miso error HOT 10
- `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` HOT 7
- RNA splice output
- Merged genes output HOT 3
- DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER not working with special characters in sample names
- AWSmegatests are failing HOT 5
- Spare memory for samtools issue HOT 1
- Implement IsoformSwitchAnalyzeR HOT 2
- Miso ERROR HOT 12
- Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FEATURECOUNTS (SRX12134688)', Caused by: Process `NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FEATURECOUNTS (SRX12134688)` terminated with an error exit status (255) HOT 32
- Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:RMATS:CREATE_BAMLIST_SINGLE (1)' caused by: No such variable: bam -- Check script '/home/tud03125/.nextflow/assets/nf-core/rnasplice/./workflows/../subworkflows/local/../../modules/local/create_bamlist_single.nf' at line: 20 HOT 1
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