Demo data run error--no coverage at region? #67
Description
Hi,
I downloaded and tried to run the demo data. I get an error stating that the smn region doesn't appear to have coverage (and something about invalid scalar divide). I did download the bam + bai and verify that there were reads at smn1. I also tried my own bam file, also with similar null results.
Thanks!
paraphase -b ./paraphase/tests/test_data/HG01175_smn1_extracted.bam -r ./human_GRCh38_no_alt_analysis_set/human_GRCh38_no_alt_analysis_set.fasta -o ./output/ -p HG01175 -g smn1
INFO:root:Processing sample HG01175 at 2026-01-16 12:19:48.973574...
INFO:root:Getting genome depth for sample HG01175 at 2026-01-16 12:19:48.973861...
/Users/miniconda3/lib/python3.13/site-packages/paraphase/genome_depth.py:59: RuntimeWarning: invalid value encountered in scalar divide
self.mad = np.median([abs(a - self.mdepth) for a in depth]) / self.mdepth
WARNING:root:For sample HG01175, due to low or highly variable genome coverage, genome coverage is not used for depth correction.
INFO:root:Running analysis for smn1 for sample HG01175 at 2026-01-16 12:19:48.977860...
INFO:root:Realigning reads for smn1 for sample HG01175 at 2026-01-16 12:19:48.977896...
INFO:root:Phasing haplotypes for smn1 for sample HG01175 at 2026-01-16 12:20:07.275398...
WARNING:root:This region does not appear to have coverage. Will not attempt to phase haplotypes.
INFO:root:Tagging reads for smn1 for sample HG01175 at 2026-01-16 12:20:07.548070...
INFO:root:Realigning to gene2 region for smn1 for sample HG01175 at 2026-01-16 12:20:23.255098...
INFO:root:Generating VCFs for smn1 for sample HG01175 at 2026-01-16 12:20:49.104027...
INFO:root:Merging all bams for sample HG01175 at 2026-01-16 12:20:49.221603...
INFO:root:Writing to json for sample HG01175 at 2026-01-16 12:21:20.425654...
INFO:root:Completed Paraphase analysis at 2026-01-16 12:21:36.924969...