Long read error - Githubissues

Dear author,

Thanks for developing this tool! I am using the command below to genotype SVs.

jellyfish count --canonical --lower-count 2 --out-counter-len 2 --mer-len 25 --threads 8 --size 3G --output counts.jf ./hg38/no_alt/hg38.no_alt.fa

locityper add -d db -r ./hg38/no_alt/hg38.no_alt.fa -j counts.jf -v ./mc/hprc-v1.1-grch38.vcf.gz -l test_region chr22:42106499-42160865

locityper preproc -a ./GRCh38/PacBio_HiFi/HG01890.all.sorted.bam -j counts.jf -r ./hg38/no_alt/hg38.no_alt.fa -o HG01890 -t hifi

The first two commands work well, but an error raised when I run the final step.

[16:13:37 DEBUG] locityper v0.10.9-1 @ 2023-11-07 16:13:37
[16:13:37  INFO] Recognized GRCh38 reference genome, using background region chr17:72062001-76562000
[16:13:37  INFO] Detected jellyfish k-mer size: 25
[16:13:37  INFO] Calculating k-mer counts on the background region
[16:13:43 DEBUG] Loading mapped reads into memory (./GRCh38/PacBio_HiFi/HG01890
.all.sorted.bam)
[16:13:46 DEBUG]     Loaded 18201 alignments, discarded 692
[16:13:46 DEBUG]     Using 5000 bp windows, (window neighbourhood size 5000, boundary 1000)
[16:13:46 DEBUG]     Total windows:       899
[16:13:46 DEBUG]     Remove 0 windows with Ns, 672 windows with common k-mers
[16:13:46 DEBUG]     After filtering:     227
[16:13:46  INFO] Estimating read error profiles from 18201 reads
[16:13:46  INFO]         69449915 matches    (0.993567)
[16:13:46  INFO]            86444 mismatches (0.001237)
[16:13:46  INFO]           224809 insertions (0.003216)
[16:13:46  INFO]           138437 deletions  (0.001981)
[16:13:46  INFO]     Maximum allowed edit distance: 469 (for read length 15000, 99%-confidence interval)
[16:13:47  INFO]     Read depth mean = 39.73,  variance: 71.09  (at GC-content 40)
[16:13:47  INFO] Success. Total time: 0:00:10.392

tprodanov / locityper

Long read error #2