Support Request: Index Error in UROPA Annotation

[cammo0p]

I encountered an issue while running the pipeline and wanted to raise a ticket.

I first tested the pipeline using the example.config file with the example dataset, and it ran successfully. However, when I used my sample data, the pipeline stopped at the UROPA annotation step, showing an IndexError (as attached : Sample1_2024-11-28T173214.935300.snakemake.log.

The issue seems related to a specific workflow step but could potentially be sample-specific, as the example dataset worked fine. Below are the input files I supplied:

• reference.fasta
• reference.fasta.fai
• reference.gtf
• sample.bw
• sample.bed
• JASPAR2024_CORE_non-redundant_pfms_jaspar.txt

Would you be able to provide insight into what might be causing this error? Thank you for your help.

Best,
Chloe

[hschult]

Hi Chloe, thank you for your interest in DENIS.

Which snakemake version are you running? This may be related to #1 so please make sure to have a snakemake version between >=7.15.2 and <8. If this is already the case my next guess is that there is something wrong with the binding site annotation process. The reason could be a problem with the input query, which you specify through uropa_template.json. Please make sure that the features defined in the .json are available in your reference.gtf. You may also look at the output_dir/logs/uropa/motif_18_motif_18.log (feel free to send it) this could give additional insight into the issue.

Best wishes,
Hendrik