Hi all, thanks for this channel and the tools! I’m new to proteomics (and nextflow), and have been struggling to get the pipeline to run through to completion (which I am using on an HPC cluster). I ran the test example just fine, but when I try to use it on my own data, it seems to stop an the ProteomicsLFQ step. I believe this is because after psm and peptide fdr, there are not any reliable hits with q<0.1 ? I have tried changing all the FDR thresholds to be more permissive (such as 0.05), using multiple search engines (sage, msgf, and comet) to generate more peaks, or using percolator versus fit_distribution for the posterior probabilities but none of those changes or combinations therein help. When I check the debugging steps in the work directory, it seems like plfq is getting little or no input despite there being many spectra with many positive hits. I’m not sure if I’m doing something wrong with the pipeline, or maybe my initial data input and parameters, but I could use any advice. I’m attaching some of the outputs, and can attach more if requested. For context, I am trying to identify and quantify within a sample (relatively) the secreted proteins from a species, looking across multiple species and matching up each of their secretions to to their translated transcriptomes. For some species, I have multiple samples, but for most I only have 1 LC-MS sample. I am mostly concerned with detecting what is in the secretion, even if all I can do is confidently confirm the presence of certain proteins from the transcriptomes. I’m not a proteomics person generally, and am just getting started using such analyses. Here’s a copy of my command line call to nextflow: nextflow run bigbio/quantms -r dev -c /home/nf_quantms/quantms/nextflow_copy.config \ --input /home/nf_quantms/SVU_Maristella_Belize_JAG/svu_maristella_exp_setup.sdrf.tsv \ --outdir /home/nf_quantms/SVU_Maristella_Belize_JAG/ \ --multiqc_title SVU_Maristella_Belize_JAG \ --database /home/nf_quantms/SVU_Maristella_Belize_JAG/SVU_Maristella_cdhit_95_uw_contamination.fasta \ -profile mamba