Hi, I am running the nf-core/pixelator pipeline (v2.3.1) on the Bianca (UPPMAX) cluster with 8 samples and facing persistent issues with high-memory steps. I initially tested the pipeline with a single sample, and it completed successfully. However, when running with multiple samples, some processes (especially nf-NFCORE_PIXELATOR_PIXEL / PIXELATOR_PNA_GRAPH) frequently fail with exit status 137 (out-of-memory) on standard nodes. To address this, I tried requesting fat nodes (mem256GB). But I started encountering submission errors such as: “Error submitting process … Execution is retried” In this situation, only the main job runs, while the sub-processes remain pending or repeatedly retry. As a result, the pipeline does not progress. I would appreciate your guidance on the following: 1. What is the recommended way to run nf-core/pixelator on Bianca when more than 128 GB memory is required? 2. Are there any special settings needed for running this pipeline on fat nodes with Nextflow/Slurm? Thank you very much in advance for your support. Best regards, Indranil

Using the uppmax profile should pick up whatever is needed to deal with various nodes automatically. Have you seen that the

memory

for the problematic process is set high enough?