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Recommendations for running EGAPx with hundreds of RNA-seq datasets on an HPC cluster

Status: Open.

#261 In ncbi/egapx;

· zhoudreames opened on Jul 31, 2026

Local SRA read cache isn't relocatable — read paths in sra_dir/runs.yaml are stored as absolute paths

Status: Open.

#257 In ncbi/egapx;

· richard-burhans opened on Jun 18, 2026

rnaseq_collapse fails with a CStringException::eConvert error

Status: Open.

#256 In ncbi/egapx;

· ymilesz opened on Jun 15, 2026

On the masking step

Status: Open.

#253 In ncbi/egapx;

· DaniPaulo opened on Jun 5, 2026

Newer nextflow version (26.04.x) import errors

Status: Open.

#251 In ncbi/egapx;

· brantfaircloth opened on Jun 2, 2026

Memory Configuration Issues for Large Genomes

Status: Open.

#250 In ncbi/egapx;

· biolittleboy opened on Jun 1, 2026

star_wnode writes ~5.5 TB of temporary files to disk when TMPDIR is set in slurm.config

Status: Open.

#249 In ncbi/egapx;

· nicolasmalexandre opened on May 29, 2026

Segmentation fault in rnaseq_collapse

Status: Open.

#246 In ncbi/egapx;

· ld9866 opened on May 14, 2026

‌Arabidopsis thaliana rnaseq_collapse Segmentation fault

Status: Open.

#245 In ncbi/egapx;

· kingbin97 opened on May 12, 2026

*** EGAPx v0.5.2 Notice ***

Status: Open.

#236 In ncbi/egapx;

· pstrope opened on Apr 24, 2026

Download genome as part of Offline mode?

Status: Open.

#220 In ncbi/egapx;

· richard-burhans opened on Apr 8, 2026

Isoform nomenclature question

Status: Open.

#217 In ncbi/egapx;

· MonicaPoelchau-USDA opened on Mar 24, 2026