I am encountering the following error when executing the Seeker Primary Analysis Pipeline. What’s wrong?

I am encountering the following error when executing the Seeker Primary Analysis Pipeline. What’s wrong?

NOTE: Process `NF:CURIOSEEKER:PRIMARY_READ1:CURIOSEEKER_CALCULATETOPBB_COMBINED (Mouse_spleen_1M)` terminated with an error exit status (255) -- Execution is retried (1) 

NOTE: Process `NF:CURIOSEEKER:PRIMARY_READ1:CURIOSEEKER_CALCULATETOPBB_COMBINED (Mouse_spleen_1M)` terminated with an error exit status (255) -- Error is ignored 

Join mismatch for the following entries: key=[id:Mouse_spleen_1M, sample:Mouse_spleen_1M, experiment_date:2023-09-26, barcode_file:/curio_example/example_input_mouse_spleen_1M/A0010_039_BeadBarcodes.txt, single_end:false, genome:GRCm38, gtf:/cluster/reference_mouse//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf, star_index:/reference_mouse//Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/, report:b] values=[/curio_example/example_input_mouse_spleen_1M/A0010_039_BeadBarcodes.txt] 

-[nf-core/curioseeker] Pipeline completed with errors- 

WARN: Killing running tasks (1) 

 

  • In this case, curio_seeker_singularity parameter in the nextflow.config was improperly formatted (see example below). Correct the formatting before proceeding. 
  • In this example, there are five forward slashes ('/') after 'file:', when there should be only four. 

curio_seeker_singularity 

file://///home/user/curioseeker-v3.0.0/.singularity/ 

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