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find-motifs stuck in loop? #360

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Ge0rges opened this issue Jan 31, 2025 · 2 comments
Open

find-motifs stuck in loop? #360

Ge0rges opened this issue Jan 31, 2025 · 2 comments
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@Ge0rges
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Ge0rges commented Jan 31, 2025

Hi @ArtRand,

I'm doing the following in find-motifs --contig, attach with the head of the log:

[src/logging.rs::60][2025-01-30 19:36:44][DEBUG] command line: modkit find-motifs --min-coverage 5 -i methylation_data//metagenome_assembly/all_samples.bed.gz -r mags/metagenome_assembly.fna --contig contig_100151 -o methylation_data//metagenome_assembly/motifs/5_contig_100151_motifs.tsv --log-filepath methylation_data//metagenome_assembly/motifs/5_contig_100151_motifs.tsv.log --threads 20
[src/find_motifs/mod.rs::971][2025-01-30 19:36:44][INFO] loading references from "mags/metagenome_assembly.fna"
[src/find_motifs/mod.rs::1002][2025-01-30 19:36:49][INFO] loaded 106135 sequence(s)
[src/find_motifs/mod.rs::1132][2025-01-30 19:36:49][INFO] using tabix/bgzf reader
[src/find_motifs/mod.rs::1240][2025-01-30 19:36:50][INFO] parsed 576 bedmethyl records, discarded 20449 for low coverage, 21025 total
[src/find_motifs/mod.rs::1327][2025-01-30 19:36:50][INFO] loaded 406 low-frequency, 2 middle-frequency and 93 high-frequency contexts, 3 modification codes, discarded 0 contexts.
[src/find_motifs/mod.rs::736][2025-01-30 19:36:50][DEBUG] inferred C associated with modification code m
[src/find_motifs/mod.rs::736][2025-01-30 19:36:50][DEBUG] inferred A associated with modification code a
[src/find_motifs/mod.rs::736][2025-01-30 19:36:50][DEBUG] inferred C associated with modification code 21839
[src/find_motifs/mod.rs::2329][2025-01-30 19:36:50][DEBUG] at start for mod a there are 0 high contexts and 244 low contexts
[src/find_motifs/mod.rs::2329][2025-01-30 19:36:50][DEBUG] at start for mod m there are 93 high contexts and 72 low contexts
[src/find_motifs/mod.rs::2329][2025-01-30 19:36:50][DEBUG] at start for mod 21839 there are 0 high contexts and 165 low contexts
[src/find_motifs/mod.rs::2205][2025-01-30 19:36:50][DEBUG] zero fixed length motifs, finished in 1 iterations
[src/find_motifs/mod.rs::2348][2025-01-30 19:36:50][DEBUG] (a) seeded motifs didn't find any motifs, took 0ms
[src/find_motifs/mod.rs::2205][2025-01-30 19:36:50][DEBUG] zero fixed length motifs, finished in 1 iterations
[src/find_motifs/mod.rs::2348][2025-01-30 19:36:50][DEBUG] (m) seeded motifs didn't find any motifs, took 0ms
[src/find_motifs/mod.rs::2205][2025-01-30 19:36:50][DEBUG] zero fixed length motifs, finished in 1 iterations
[src/find_motifs/mod.rs::2348][2025-01-30 19:36:50][DEBUG] (21839) seeded motifs didn't find any motifs, took 0ms
[src/find_motifs/mod.rs::1918][2025-01-30 19:36:50][DEBUG] no changes, finished refining [a] into [a], took 0 iterations
[src/find_motifs/mod.rs::1918][2025-01-30 19:36:50][DEBUG] no changes, finished refining [m] into [m], took 0 iterations
[src/find_motifs/mod.rs::1918][2025-01-30 19:36:50][DEBUG] no changes, finished refining [21839] into [21839], took 0 iterations
[src/find_motifs/mod.rs::2401][2025-01-30 19:36:50][DEBUG] (a) done searching for seedless motifs, found 1
[src/find_motifs/mod.rs::2411][2025-01-30 19:36:50][DEBUG] performing search
[src/find_motifs/mod.rs::2401][2025-01-30 19:36:50][DEBUG] (21839) done searching for seedless motifs, found 1
[src/find_motifs/mod.rs::2401][2025-01-30 19:36:50][DEBUG] (m) done searching for seedless motifs, found 1
[src/find_motifs/mod.rs::2411][2025-01-30 19:36:50][DEBUG] performing search
[src/find_motifs/mod.rs::2411][2025-01-30 19:36:50][DEBUG] performing search
[src/find_motifs/mod.rs::603][2025-01-30 19:36:50][DEBUG] creating bool tables took 2515 ms
[src/find_motifs/mod.rs::603][2025-01-30 19:36:50][DEBUG] creating bool tables took 2656 ms
[src/find_motifs/mod.rs::603][2025-01-30 19:36:50][DEBUG] creating bool tables took 3962 ms

I've noticed that this specific contig in the past has caused the program to seemingly hang for days. I'm revisiting this issue currently.
The log file is actively being printed to after 3h of processing this contig, here's the tail of the log:

[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (6) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNK
 [(1.0, 6, -9, 71), (1.0, 3, -9, 84), (1.0, 6, 9, 71), (1.0, 3, 9, 84)], picking arbitrary position? Bases are also the same.
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif CNNNNNNNNNT[m]NNNNR
 [(1.0, 3, 5, 65), (1.0, 3, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif KNNNNNNNN[m]NNNNNGNNT
 [(1.0, 3, -9, 71), (1.0, 3, -9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (9) and frac (1) mod for motif YNNNNNNNNNY[m]NNNNR
 [(0.9166667, 11, -11, 67), (1.0, 9, -11, 84), (0.93333334, 14, -1, 67), (1.0, 6, -1, 84), (1.0, 9, 5, 65), (0.9166667, 11, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (2) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNA
 [(1.0, 2, -11, 67), (1.0, 2, -11, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0, 3, -11, 84), (1.0, 2, 5, 65), (1.0, 4, 5, 71)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (7) and frac (1) mod for motif BNNNNNNNN[m]NNNNNGNNW
 [(0.9166667, 11, -9, 67), (1.0, 7, -9, 71), (0.8888889, 8, -9, 84), (1.0, 7, 9, 65), (0.85714287, 6, 9, 84)], picking arbitrary position?
[src/find_motifs/mod.rs::1851][2025-01-30 19:38:08][DEBUG] same number of high-mod sites (3) and frac (1) mod for motif YNNNNNNNNNC[m]NNNNR
 [(1.0, 3, -11, 67), (1.0

If I'm not mistaken, it seems like it's perhaps stuck in a loop?

The program output in terminal is:

> loading references from "mags/metagenome_assembly.fna"
> loaded 106135 sequence(s)
> using tabix/bgzf reader
> parsed 576 bedmethyl records, discarded 20449 for low coverage, 21025 total
> loaded 406 low-frequency, 2 middle-frequency and 93 high-frequency contexts, 3 modification codes, discarded 0 contexts.
[00:00:00] ########################################  129403/129536  (a) seeds searched
[00:00:09] ########################################  128803/129536  (m) seeds searched
[00:00:00] ########################################  129377/129536  (21839) seeds searched

The contig is not excessively long, at 22158 bp. Is it possible the program is stuck in an infinite loop?
@ArtRand
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ArtRand commented Jan 31, 2025

Hello @Ge0rges,

Just to be sure, if you use --skip-search does the routine finish? Would you be willing to send me the contig sequence and the bedMethyl? I need to debug it. I don't know for sure, but I think multithreading makes the logs difficult to interpret (although your diagnosis is correct). Thanks!

@ArtRand ArtRand added the bug Something isn't working label Jan 31, 2025
@Ge0rges
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Ge0rges commented Feb 1, 2025 •
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Hey Art,

Looks like this exited after a day (with insufficient coverage error)... perhaps I reacted too soon. I can still share these with you to check.

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