Closed JunlyMa closed 5 months ago
starskyzheng
commented
7 months ago PanPop utilized snakemake to support parallel running and even running on cluster. You could read wiki of snakemake (https://snakemake.readthedocs.io/en/stable/) or just use PanPop for convinent.
JunlyMa
commented
7 months ago Thank you, I have learned some snake content, which has greatly improved my use of this program.. However, I found that a small number of samples always reach the generation of 2.callSV/.gaffe.aug.pg, .gaffe.aug.gam, .gaffe.aug.snarls, .gaffe.aug.q5.pack, and .gaffe.aug.q5.pack.DPinfo. And the generated .gaffe.aug.q5.call.ext.vcf.gz file is empty, but the program keeps running (it has been running for two days and still has no output, other normal samples will normally output .gaffe.aug.q5.call.ext.vcf.gz and .gaffe.aug.q5.call.vcf.gz files within 2-4 hours). After running these samples from the beginning many times, they are always stuck at this step, and the reason has not been found.
starskyzheng
commented
7 months ago Maybe the reads.fq.gz were incomplete?
github-actions[bot]
commented
6 months ago This issue is stale because it has been open for 30 days with no activity.
github-actions[bot]
commented
5 months ago This issue was closed because it has been inactive for 14 days since being marked as stale.
Dear @starskyzheng,
Panpop is a powerful software for identifying structural variants (SVs) in next-generation sequencing (NGS) data, and I truly appreciate your work in developing this software. However, I'm facing an issue where I can only analyze one sample at a time when using the software to analyze NGS SVs. I haven't been able to find a batch submission method similar to submitting a for-loop script. Can Panpop handle parallel processing of multiple NGS samples to simultaneously generate files like ".gaffe.gam", ".gaffe.aug.gam", ".gaffe.aug.pg", etc.? Currently, I have over two hundred samples, and the speed is too slow. How should I proceed to utilize parallel computing?
Thank you very much.