PINTS tasks stall when FASTA includes GL/KI contigs; works after restricting to chr

### Description of the bug When running nf-core/nascent (v2.3.0) on human GRO‑seq data with a GRCh38 FASTA that includes additional scaffold / patch / decoy contigs (e.g. GL000226.1, KI27044*.1, etc.), the workflow creates 300+ PINTS shard processes (one per contig). PINTS shards for small/non‑standard contigs fail with “No signal found across all chromosomes!” and overall progress stalls; the run hits walltime (7 days) with PINTS_CALLER still at 0 of 384 or only a few completed. After producing a FASTA restricted to the 24 canonical chromosomes + MT + common alt (total 46 entries in my chrOnly file), the pipeline finishes successfully in ~14 hours, skipping groHMM or less than 7 days, including groHMM. ### Command used and terminal output ```console #!/bin/bash #SBATCH --time=6-23:59:59 #SBATCH --mem=130G #SBATCH --nodes=1 #SBATCH --job-name=GROseq #SBATCH --partition=unmc_cbsb #SBATCH --output=job_%A_%a.out #SBATCH --error=job_%A_%a.err #SBATCH --cpus-per-task=30 export NXF_OPTS='-Xms16g -Xmx50g' module load singularity/3.8 module load nextflow/24.04 export NXF_SINGULARITY_CACHEDIR=/lustre/work/unmc_cbsb/saadyeh/singularity_cache export NXF_SINGULARITY_RUN_OPTIONS="--no-mount common" nextflow run nf-core/nascent \ -r 2.3.0 \ -profile singularity \ --input GRO_samplesheet.csv \ --outdir results/groseq \ --fasta GRCh38.chrOnly.fa \ --gtf merged_final_noCDS.gtf \ --assay_type GROseq \ --save_reference \ -resume [14/759628] NFCâ€merged_final_noCDS.gtf) | 1 of 1, cached: 1 ✔ [86/139949] NFC…MSIZES (GRCh38.chrOnly.fa) | 1 of 1, cached: 1 ✔ [44/92e43f] NFC…_INDEX (GRCh38.chrOnly.fa) | 1 of 1, cached: 1 ✔ [3a/dc82a9] NFC…:NASCENT:FASTQC (MYC_REP2) | 4 of 4, cached: 4 ✔ [af/287771] NFC…SCENT:FASTP (CONTROL_REP2) | 4 of 4, cached: 4 ✔ [2b/9f1486] NFC…BWA:BWA_MEM (CONTROL_REP2) | 4 of 4, cached: 4 ✔ [8b/522264] NFC…MTOOLS_SORT (CONTROL_REP2) | 4 of 4, cached: 4 ✔ [ee/d89769] NFC…TOOLS_INDEX (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [6e/15054b] NFC…TOOLS_STATS (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [b7/cfd876] NFC…MTOOLS_FLAGSTAT (MYC_REP2) | 4 of 4, cached: 4 ✔ [99/a45512] NFC…MTOOLS_IDXSTATS (MYC_REP2) | 4 of 4, cached: 4 ✔ [27/9b10d0] NFC…ESEQ_CCURVE (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [06/fd7d9b] NFC…EQ_LCEXTRAP (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [c5/6dec26] NFC…REXPERIMENT (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [75/93c8ef] NFC…ISTRIBUTION (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [51/655e91] NFC…DUPLICATION (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [c6/595ad3] NFC…BMAP_PILEUP (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [52/609d91] NFC…OMECOV_PLUS (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [5b/8f8c1a] NFC…MECOV_MINUS (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [26/e44082] NFC…VERAGE_PLUS (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [90/a102dc] NFC…ERAGE_MINUS (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [9f/659c18] NFC…S:DREG_PREP (CONTROL_REP1) | 4 of 4, cached: 4 ✔ [94/910640] NFC…AMETERTUNING (MYC|45|-300) | 126 of 126, cached: 114 ✔ [e5/7db1a0] NFC…RANSCRIPTCALLING (CONTROL) | 2 of 2 ✔ [96/b7fd1f] NFC…MAKETAGDIRECTORY (CONTROL) | 2 of 2, cached: 2 ✔ [1c/599633] NFC…MER_MAKEUCSCFILE (CONTROL) | 2 of 2, cached: 2 ✔ [b4/e26240] NFC…:HOMER_FINDPEAKS (CONTROL) | 2 of 2, cached: 2 ✔ [9d/796333] NFC…EQ:HOMER_POS2BED (CONTROL) | 2 of 2, cached: 2 ✔ [c1/15c04e] NFC…N:SAMTOOLS_MERGE (CONTROL) | 2 of 2, cached: 2 ✔ [bc/13a63b] NFC…:PINTS_CALLER (MYC | chrX) | 46 of 46 ✔ [67/e91c28] NFC…FICATION:CAT_CAT (CONTROL) | 2 of 2 ✔ [8c/f53b16] NFC…ON:BEDTOOLS_SORT (CONTROL) | 2 of 2 ✔ [e4/0d244a] NFC…N:BEDTOOLS_MERGE (CONTROL) | 2 of 2 ✔ [de/568917] NFC…:NASCENT:BED2SAF (CONTROL) | 6 of 6, cached: 2 ✔ [7e/fb7993] NFC…TURECOUNTS_PREDICTED (MYC) | 12 of 12, cached: 4 ✔ [8e/abe0f3] NFC…D_FEATURECOUNTS_GENE (MYC) | 2 of 2, cached: 2 ✔ [45/c9ee9e] NFCORE_NASCENT:NASCENT:MULTIQC | 1 of 1 ✔ -[nf-core/nascent] Pipeline completed successfully- Completed at: 13-Jul-2025 12:22:42 Duration : 1d 19h 46m 38s CPU hours : 1'932.1 (72.8% cached) Succeeded : 79 Cached : 211 ``` ### Relevant files _No response_ ### System information Nextflow version: nextflow/24.04 singularity/3.8 HPC Version of nf-core/nascent: 2.3.0