sourmash gather found less than 50.0 kbp in common

[LeahRoberts]

Hi Gerry,

I just wanted to check an error that was thrown on some of my samples.

When running "find references" with Sourmash, it throws the following error:

2025-01-15 16:20:00 - INFO - finding references...
2025-01-15 16:20:00 - INFO - command: sourmash gather -o /mnt/hpccs01/home/roberl24/work/TBA_ICU/timepoint_2/tracs/LR39_S24_align/LR39_S24_sourmash_hits.csv --threshold-bp 50000 --ignore-abundance /mnt/hpccs01/home/roberl24/work/TBA_ICU/timepoint_2/tracs/LR39_S24_align/tmph_gal72f/query.sig /home/roberl24/gtdb-rs214-reps.k51.sbt.zip

== This is sourmash version 4.8.12. ==
== Please cite Irber et. al (2024), doi:10.21105/joss.06830. ==

select query k=51 automatically.
loaded query: query... (k=51, DNA)
--
loaded 85205 total signatures from 1 locations.
after selecting signatures compatible with search, 85205 remain.
Starting prefetch sweep across databases.
Prefetch found 0 signatures with overlap >= 50.0 kbp.
Doing gather to generate minimum metagenome cover.
found less than 50.0 kbp in common. => exiting

No matches found for --threshold-bp at 50.0 kbp.
Traceback (most recent call last):
  File "/home/roberl24/miniforge3/envs/tracs/bin/tracs", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/roberl24/miniforge3/envs/tracs/lib/python3.12/site-packages/tracs/__main__.py", line 55, in main
    func(args)
  File "/home/roberl24/miniforge3/envs/tracs/lib/python3.12/site-packages/tracs/align.py", line 351, in align
    references = run_gather(
                 ^^^^^^^^^^^
  File "/home/roberl24/miniforge3/envs/tracs/lib/python3.12/site-packages/tracs/utils.py", line 61, in run_gather
    with open(output + ".csv", "r") as infile:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/hpccs01/home/roberl24/work/TBA_ICU/timepoint_2/tracs/LR39_S24_align/LR39_S24_sourmash_hits.csv'

Just wanted to check that this means Sourmash could not find an appropriate reference genome. Is that right?

[gtonkinhill]

Hi Leah,

Yes, that's correct, although it should exit more gracefully than that! I'll look into adding a better warning message.