Closed sme229 closed 1 month ago
Hi @sme229
The error message below tells us that the expression matrix is empty
The expression matrix contains no cells.
This may indicate an issue with data quality or volume.
Incorrectly specified 10x kits/versions and reference data can also lead to
to removal of all data at this point.
Have you specified the correct kit and version? Does the reference sequence have the correct matching annotation? How many reads are trying to process?
Hello @nrhorner
Thanks for looking into this. The kit version is actually v3.1, I'll try to run with 3.1 instead of 3.
This is how my reference fasta file looks like:
I modified the headers in my reference file and that seemed to solve the issue, but I get a different error now. I'll open a new issue
Operating System
Other Linux (please specify below)
Other Linux
Linux 5.14.21-150400.24.28-default
Workflow Version
wf-single-cell v2.1.0-ga25ec6c
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
wf-single-cell v2.1.0-ga25ec6c
CLI command run
nextflow run epi2me-labs/wf-single-cell --expected_cells 3000 -profile singularity --fastq 'Elena-cDNA-2/20240624_1312_1D_PAW58377_76308a2c/fastq_pass' --kit_name '3prime' --kit_version 'v3' --ref_genome_dir 'OryCun_genome'
Workflow Execution - CLI Execution Profile
None
What happened?
Hello, I've got this error: Traceback (most recent call last): File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow-glue", line 7, in
cli()
File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/init.py", line 82, in cli
args.func(args)
File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/process_matrix.py", line 106, in main
raise ValueError("""The expression matrix contains no cells.
ValueError: The expression matrix contains no cells.
This may indicate an issue with data quality or volume.
Incorrectly specified 10x kits/versions and reference data can also lead to
to removal of all data at this point.
I couldn't find the exact same error in resolved issues. I also attach a screenshot my gtf file.
![gtf_file](https://github.com/user-attachments/assets/d9b11428-4ca3-4089-bf8b-50da94b86f64)
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response