gff from sRNAbench output - invalid literal error

[jonahcullen]

Expected behavior and actual behavior.

I am attempting to use mirtop gff from the output of sRNAbench. I expect a GFF to be returned. I am able to get this to work with the output from miraligner.

Steps to reproduce the problem.

mirtop gff --format srnabench --sps eca --hairpin hairpin.fa --gtf eca.gff3 -o HERE ../LocalTEST/

returns

04/11/2023 03:21:21 INFO Run annotation
Traceback (most recent call last):
  File "/opt/conda/envs/small/bin/mirtop", line 10, in <module>
    sys.exit(main())
  File "/opt/conda/envs/small/lib/python3.10/site-packages/mirtop/command_line.py", line 31, in main
    reader(kwargs["args"])
  File "/opt/conda/envs/small/lib/python3.10/site-packages/mirtop/gff/__init__.py", line 49, in reader
    out_dts[fn] = srnabench.read_file(fn, args)
  File "/opt/conda/envs/small/lib/python3.10/site-packages/mirtop/importer/srnabench.py", line 47, in read_file
    source_iso = _read_iso(reads_iso)
  File "/opt/conda/envs/small/lib/python3.10/site-packages/mirtop/importer/srnabench.py", line 169, in _read_iso
    iso[(cols[0], m)] = _translate(anno[m], cols[4])
  File "/opt/conda/envs/small/lib/python3.10/site-packages/mirtop/importer/srnabench.py", line 206, in _translate
    iso.extend(_iso_snp(int(nt.split(":")[0])))
ValueError: invalid literal for int() with base 10: '-$16'

Specifications like the version of the project, operating system, or hardware.

I am using mirtop (0.4.25) and sRNAbench.jar (2.0) on a university HPC running CentOS Linux 7.

Thanks for your time, Jonah.