Cannot combine dicts

[pdimens]

Hello again, I'm getting an error running naibr regarding combining dicts:

Traceback (most recent call last):
  File "/home/pd348/miniconda3/envs/harpy/bin/naibr", line 10, in <module>
    sys.exit(main())
  File "/home/pd348/miniconda3/envs/harpy/lib/python3.9/site-packages/naibr/__main__.py", line 391, in main
    return run(file_configs)
  File "/home/pd348/miniconda3/envs/harpy/lib/python3.9/site-packages/naibr/__main__.py", line 350, in run
    novel_adjacencies = run_naibr_on_chromosomes(chromosomes, configs)
  File "/home/pd348/miniconda3/envs/harpy/lib/python3.9/site-packages/naibr/__main__.py", line 147, in run_naibr_on_chromosomes
    linkedreads_by_barcode.combine(linkedreads_by_barcode_chrom)
  File "/home/pd348/miniconda3/envs/harpy/lib/python3.9/site-packages/naibr/__main__.py", line 294, in combine
    raise TypeError(f"Can only combine with other UnionDicts or defaultdicts ({type(other)})")
TypeError: Can only combine with other UnionDicts or defaultdicts (<class 'NoneType'>)

While itself not super informative, I think this may be due to one of the chromosomes having no candidates identified. Here's what I think may be a relevant excerpt from the log:

2023-10-11 13:19:26,225 - INFO: No candidates from Y

If I'm understanding what's happening, I think naibr assumes there will always be candidates for each chromosome and therefore doesn't have a condition to skip an empty dict?

Otherwise, the entire log is:

========= NAIBR =========
version: 0.5
-------- CONFIGS --------
FILES
  bam_file = Variants/naibr-pop/input/ZS10-221221-15x_1M.bam
  candidates = None
  blacklist = None
  outdir = Variants/naibr-pop/ZS10-221221-15x_1M
  prefix = ZS10-221221-15x_1M
PARAMETERS
  d =           150,000
  min_mapq =         30
  k =                 3
  min_sv =        1,000
  sd_mult =           2
  min_len =         806
  max_len =     200,000
  min_reads =         2
  min_discs =         2
  threads =           8
  DEBUG =         False
-------------------------
2023-10-11 13:19:26,173 - INFO: Found 7 chromosomes with data in BAM
2023-10-11 13:19:26,198 - INFO: running on 8 threads
2023-10-11 13:19:26,200 - INFO: Getting candidates for chromosome 2L
2023-10-11 13:19:26,200 - INFO: Getting candidates for chromosome 3L
2023-10-11 13:19:26,200 - INFO: Getting candidates for chromosome 2R
2023-10-11 13:19:26,200 - INFO: Getting candidates for chromosome 3R
2023-10-11 13:19:26,200 - INFO: Getting candidates for chromosome 4
2023-10-11 13:19:26,201 - INFO: Getting candidates for chromosome Y
2023-10-11 13:19:26,201 - INFO: Getting candidates for chromosome X
2023-10-11 13:19:26,222 - INFO: Done reading chromosome Y: coverage = 0.040X
2023-10-11 13:19:26,222 - INFO: Y: total pairs: 676, discordant: 4 (0.59%), concordant: 650 (96.15%)
2023-10-11 13:19:26,222 - INFO: For chromsome Y - found 16 positions with discordant reads.
2023-10-11 13:19:26,225 - INFO: Got candidate noval adjacencies from data: 0.0023 s
2023-10-11 13:19:26,225 - INFO: No candidates from Y
2023-10-11 13:19:26,282 - INFO: Done reading chromosome 4: coverage = 0.661X
2023-10-11 13:19:26,282 - INFO: 4: total pairs: 4,024, discordant: 18 (0.45%), concordant: 3,903 (96.99%)
2023-10-11 13:19:26,283 - INFO: For chromsome 4 - found 22 positions with discordant reads.
2023-10-11 13:19:26,332 - INFO: Got candidate noval adjacencies from data: 0.0490 s
2023-10-11 13:19:26,332 - INFO: Ranking 1 candidates from 4
2023-10-11 13:19:26,345 - WARNING: Low coverage (0.661X < 10X), the threshold value might not be accurate.
2023-10-11 13:19:27,370 - INFO: Done reading chromosome 2L: coverage = 0.584X
2023-10-11 13:19:27,370 - INFO: 2L: total pairs: 63,738, discordant: 222 (0.35%), concordant: 61,747 (96.88%)
2023-10-11 13:19:27,385 - INFO: For chromsome 2L - found 158 positions with discordant reads.
2023-10-11 13:19:27,531 - INFO: Done reading chromosome 3L: coverage = 0.551X
2023-10-11 13:19:27,532 - INFO: 3L: total pairs: 71,753, discordant: 181 (0.25%), concordant: 69,533 (96.91%)
2023-10-11 13:19:27,550 - INFO: For chromsome 3L - found 260 positions with discordant reads.
2023-10-11 13:19:27,591 - INFO: Done reading chromosome 2R: coverage = 0.548X
2023-10-11 13:19:27,592 - INFO: 2R: total pairs: 64,178, discordant: 203 (0.32%), concordant: 62,092 (96.75%)
2023-10-11 13:19:27,608 - INFO: For chromsome 2R - found 216 positions with discordant reads.
2023-10-11 13:19:27,612 - INFO: Done reading chromosome X: coverage = 0.546X
2023-10-11 13:19:27,612 - INFO: X: total pairs: 59,856, discordant: 113 (0.19%), concordant: 57,864 (96.67%)
2023-10-11 13:19:27,630 - INFO: For chromsome X - found 257 positions with discordant reads.
2023-10-11 13:19:27,695 - INFO: Done reading chromosome 3R: coverage = 0.568X
2023-10-11 13:19:27,696 - INFO: 3R: total pairs: 84,246, discordant: 142 (0.17%), concordant: 81,742 (97.03%)
2023-10-11 13:19:27,714 - INFO: For chromsome 3R - found 243 positions with discordant reads.
2023-10-11 13:19:28,001 - INFO: Got candidate noval adjacencies from data: 0.6163 s
2023-10-11 13:19:28,002 - INFO: Ranking 5 candidates from 2L
2023-10-11 13:19:28,170 - INFO: Got candidate noval adjacencies from data: 0.5402 s
2023-10-11 13:19:28,170 - INFO: Ranking 17 candidates from X
2023-10-11 13:19:28,187 - INFO: Got candidate noval adjacencies from data: 0.5795 s
2023-10-11 13:19:28,187 - INFO: Ranking 11 candidates from 2R
2023-10-11 13:19:28,200 - INFO: Got candidate noval adjacencies from data: 0.6499 s
2023-10-11 13:19:28,200 - INFO: Ranking 11 candidates from 3L
2023-10-11 13:19:28,353 - WARNING: Low coverage (0.584X < 10X), the threshold value might not be accurate.
2023-10-11 13:19:28,354 - INFO: Found 5 SVs on 2L of which 5 (100.0%) passed the threshold
2023-10-11 13:19:28,476 - INFO: Got candidate noval adjacencies from data: 0.7614 s
2023-10-11 13:19:28,476 - INFO: Ranking 17 candidates from 3R
2023-10-11 13:19:28,690 - WARNING: Low coverage (0.548X < 10X), the threshold value might not be accurate.
2023-10-11 13:19:28,690 - INFO: Found 8 SVs on 2R of which 8 (100.0%) passed the threshold
2023-10-11 13:19:28,786 - WARNING: Low coverage (0.551X < 10X), the threshold value might not be accurate.
2023-10-11 13:19:28,786 - INFO: Found 9 SVs on 3L of which 9 (100.0%) passed the threshold
2023-10-11 13:19:29,165 - WARNING: Low coverage (0.546X < 10X), the threshold value might not be accurate.
2023-10-11 13:19:29,166 - INFO: Found 10 SVs on X of which 10 (100.0%) passed the threshold
2023-10-11 13:19:29,502 - WARNING: Low coverage (0.568X < 10X), the threshold value might not be accurate.
2023-10-11 13:19:29,502 - INFO: Found 13 SVs on 3R of which 13 (100.0%) passed the threshold

[pontushojer]

Hello @pdimens,

I this using NAIBR installed from bioconda (naibr-plus)?

You had a similar issue (#7) which raised the same error for which I implemented a fix (#8). Just want to make sure this is a different issue.

[pdimens]

Oh wow, I forgot about experiencing that before! 🤦 . Yes, I'm using the install from bioconda. Has that release not been updated?

[pontushojer]

Oh wow, I forgot about experiencing that before! 🤦 . Yes, I'm using the install from bioconda. Has that release not been updated?

Haha, easy to forget these things ;) Good that its not a new bug at least.

I have not yet made a new release with the fix implemented, I will see about doing this shortly.

[pontushojer]

New release made and published on bioconda (bioconda/bioconda-recipes#43661)