HiTE stuck at “Start 3.1: Coarse-grained boundary mapping”

[ChuanzhengWei]

Hi ,

I encountered an issue while running HiTE (v3.3.3) on a plant genome (~700Mb). The pipeline appears to be stuck at Step 3.1: Coarse-grained boundary mapping. The process has been running for more than 18 hours without producing any new output files, and no error messages have been reported.

I would like to ask whether this behavior is expected.
Command used

singularity exec \
    -B $PWD:$PWD \
    /public/share/singularity/HiTE/HiTE-3.3.3.sif python /HiTE/main.py \
    --genome hite.fasta \
    --thread 96 \
    --plant 1 --recover 1 --annotate 1 \
    --out_dir ./HiTE_out \
    --work_dir ./HiTE_work

Relevant log output

2026-02-27 22:35:02,801 - /HiTE/main.py[line:519] - INFO: Start 3.1: Coarse-grained boundary mapping
2026-02-27 22:35:02,801 - /HiTE/main.py[line:531] - INFO: coarse_boundary.py  ......

No additional log messages are generated after this point.

Any suggestions would be greatly appreciated.