3 Performing Taxonomically Informed Metabolite Annotation

Adriano Rutz

3 Performing Taxonomically Informed Metabolite Annotation

Author

Adriano Rutz

Published

August 22, 2025

This vignette describes how Taxonomically Informed Metabolite Annotation is performed. If you followed all previous steps successfully, this should be a piece of cake, you deserve it!

tima::tima_full()
#> + par_def_ann_spe dispatched
#> ✔ par_def_ann_spe completed [29ms, 2.14 kB]
#> + par_def_wei_ann dispatched
#> ✔ par_def_wei_ann completed [1ms, 5.05 kB]
#> + par_def_pre_ann_gnp dispatched
#> ✔ par_def_pre_ann_gnp completed [1ms, 1.42 kB]
#> + par_def_pre_lib_sop_mer dispatched
#> ✔ par_def_pre_lib_sop_mer completed [1ms, 3.40 kB]
#> + yaml_paths dispatched
#> ✔ yaml_paths completed [1ms, 11.52 kB]
#> + par_def_pre_lib_sop_lot dispatched
#> ✔ par_def_pre_lib_sop_lot completed [1ms, 494 B]
#> + par_def_ann_mas dispatched
#> ✔ par_def_ann_mas completed [0ms, 6.09 kB]
#> + par_def_pre_lib_sop_hmd dispatched
#> ✔ par_def_pre_lib_sop_hmd completed [1ms, 492 B]
#> + par_def_fil_ann dispatched
#> ✔ par_def_fil_ann completed [1ms, 1.34 kB]
#> + par_def_pre_lib_sop_clo dispatched
#> ✔ par_def_pre_lib_sop_clo completed [1ms, 523 B]
#> + par_def_pre_lib_spe dispatched
#> ✔ par_def_pre_lib_spe completed [1ms, 1.57 kB]
#> + par_def_pre_fea_com dispatched
#> ✔ par_def_pre_fea_com completed [1ms, 358 B]
#> + par_def_cre_com dispatched
#> ✔ par_def_cre_com completed [1ms, 375 B]
#> + par_def_cre_edg_spe dispatched
#> ✔ par_def_cre_edg_spe completed [1ms, 1.42 kB]
#> + par_def_pre_fea_edg dispatched
#> ✔ par_def_pre_fea_edg completed [0ms, 706 B]
#> + par_def_pre_fea_tab dispatched
#> ✔ par_def_pre_fea_tab completed [1ms, 860 B]
#> + par_def_pre_lib_rt dispatched
#> ✔ par_def_pre_lib_rt completed [1ms, 2.05 kB]
#> + par_def_pre_ann_spe dispatched
#> ✔ par_def_pre_ann_spe completed [1ms, 1.46 kB]
#> + par_def_pre_ann_sir dispatched
#> ✔ par_def_pre_ann_sir completed [1ms, 1.93 kB]
#> + par_def_pre_tax dispatched
#> ✔ par_def_pre_tax completed [1ms, 1.51 kB]
#> + par_def_pre_lib_sop_ecm dispatched
#> ✔ par_def_pre_lib_sop_ecm completed [1ms, 492 B]
#> + paths dispatched
#> ✔ paths completed [2ms, 2.52 kB]
#> + lib_spe_exp_gnp_pre_sop dispatched
#> INFO [2025-08-22 07:26:53] Directory data/interim/libraries/sop created.
#> ✔ lib_spe_exp_gnp_pre_sop completed [548ms, 1.42 MB]
#> + lib_spe_exp_mb_pre_sop dispatched
#> ✔ lib_spe_exp_mb_pre_sop completed [307ms, 480.97 kB]
#> + lib_spe_exp_mer_pre_sop dispatched
#> ✔ lib_spe_exp_mer_pre_sop completed [557ms, 1.19 MB]
#> + lib_spe_is_wik_pre_sop dispatched
#> ✔ lib_spe_is_wik_pre_sop completed [1.2s, 37.90 MB]
#> + lib_spe_exp_mb_pre_pos dispatched
#> INFO [2025-08-22 07:26:57] Directory data/interim/libraries/spectra/exp created.
#> ✔ lib_spe_exp_mb_pre_pos completed [899ms, 19.41 MB]
#> + par_pre_par dispatched
#> ✔ par_pre_par completed [0ms, 1.38 kB]
#> + lib_spe_exp_mer_pre_neg dispatched
#> ✔ lib_spe_exp_mer_pre_neg completed [1.1s, 31.54 MB]
#> + lib_spe_is_wik_pre_neg dispatched
#> INFO [2025-08-22 07:26:59] Directory data/interim/libraries/spectra/is created.
#> ✔ lib_spe_is_wik_pre_neg completed [13.6s, 687.33 MB]
#> + par_pre_par2 dispatched
#> ✔ par_pre_par2 completed [0ms, 21.17 kB]
#> + lib_spe_is_wik_pre_pos dispatched
#> Downloading  40% ■■■■■■■■■■■■■                     2s
#> Downloading  95% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■    0s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> ✔ lib_spe_is_wik_pre_pos completed [21.8s, 863.95 MB]
#> + lib_sop_lot dispatched
#> INFO [2025-08-22 07:27:38] Downloading 230106_frozen_metadata.csv.gz from https://doi.org/10.5281/zenodo.5794106 (The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata); unique identifier: https://doi.org/10.5281/zenodo.7534071)
#> INFO [2025-08-22 07:27:38] Directory data/source/libraries/sop created.
#> ✔ lib_sop_lot completed [2m 39.1s, 92.98 MB]
#> + lib_sop_hmd dispatched
#> INFO [2025-08-22 07:30:15] Directory data/source/libraries/sop/hmdb created.
#> Downloading   1% ■                                 1m
#> Downloading   2% ■                                 2m
#> Downloading   4% ■■                                2m
#> Downloading   5% ■■■                               2m
#> Downloading   7% ■■■                               2m
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> ✔ lib_sop_hmd completed [14s, 96.48 MB]
#> + lib_spe_exp_gnp_pre_neg dispatched
#> ✔ lib_spe_exp_gnp_pre_neg completed [3.9s, 154.12 MB]
#> + lib_spe_exp_mer_pre_pos dispatched
#> ✔ lib_spe_exp_mer_pre_pos completed [1.9s, 84.94 MB]
#> + lib_sop_ecm dispatched
#> Downloading  32% ■■■■■■■■■■■                       2s
#> Downloading  97% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■    0s
#> ✔ lib_sop_ecm completed [2.3s, 1.33 MB]
#> + lib_spe_exp_mb_pre_neg dispatched
#> ✔ lib_spe_exp_mb_pre_neg completed [620ms, 7.06 MB]
#> + lib_spe_exp_gnp_pre_pos dispatched
#> ✔ lib_spe_exp_gnp_pre_pos completed [8.6s, 481.27 MB]
#> + par_fin_par dispatched
#> ✔ par_fin_par completed [1ms, 307 B]
#> + par_fin_par2 dispatched
#> ✔ par_fin_par2 completed [3ms, 2.96 kB]
#> + par_usr_pre_lib_sop_mer dispatched
#> TRACE [2025-08-22 07:30:48] Loading default params
#> TRACE [2025-08-22 07:30:48] All params
#> TRACE [2025-08-22 07:30:48] Small params
#> TRACE [2025-08-22 07:30:48] Advanced params
#> TRACE [2025-08-22 07:30:48] Changing params
#> TRACE [2025-08-22 07:30:48] Changing filenames
#> TRACE [2025-08-22 07:30:49] Exporting params
#> INFO [2025-08-22 07:30:49] Directory params/user created.
#> ✔ par_usr_pre_lib_sop_mer completed [1.4s, 1.55 kB]
#> + par_usr_pre_lib_sop_lot dispatched
#> TRACE [2025-08-22 07:30:49] Loading default params
#> TRACE [2025-08-22 07:30:49] All params
#> TRACE [2025-08-22 07:30:49] Small params
#> TRACE [2025-08-22 07:30:49] Advanced params
#> TRACE [2025-08-22 07:30:49] Changing params
#> TRACE [2025-08-22 07:30:49] Changing filenames
#> TRACE [2025-08-22 07:30:51] Exporting params
#> ✔ par_usr_pre_lib_sop_lot completed [1.3s, 174 B]
#> + par_usr_pre_tax dispatched
#> TRACE [2025-08-22 07:30:51] Loading default params
#> TRACE [2025-08-22 07:30:51] All params
#> TRACE [2025-08-22 07:30:51] Small params
#> TRACE [2025-08-22 07:30:51] Advanced params
#> TRACE [2025-08-22 07:30:51] Changing params
#> TRACE [2025-08-22 07:30:51] Changing filenames
#> TRACE [2025-08-22 07:30:52] Exporting params
#> ✔ par_usr_pre_tax completed [1.3s, 438 B]
#> + par_usr_pre_ann_gnp dispatched
#> TRACE [2025-08-22 07:30:52] Loading default params
#> TRACE [2025-08-22 07:30:52] All params
#> TRACE [2025-08-22 07:30:52] Small params
#> TRACE [2025-08-22 07:30:52] Advanced params
#> TRACE [2025-08-22 07:30:52] Changing params
#> TRACE [2025-08-22 07:30:52] Changing filenames
#> TRACE [2025-08-22 07:30:54] Exporting params
#> ✔ par_usr_pre_ann_gnp completed [1.3s, 708 B]
#> + par_usr_pre_lib_sop_hmd dispatched
#> TRACE [2025-08-22 07:30:54] Loading default params
#> TRACE [2025-08-22 07:30:54] All params
#> TRACE [2025-08-22 07:30:54] Small params
#> TRACE [2025-08-22 07:30:54] Advanced params
#> TRACE [2025-08-22 07:30:54] Changing params
#> TRACE [2025-08-22 07:30:54] Changing filenames
#> TRACE [2025-08-22 07:30:55] Exporting params
#> ✔ par_usr_pre_lib_sop_hmd completed [1.3s, 178 B]
#> + par_usr_cre_com dispatched
#> TRACE [2025-08-22 07:30:55] Loading default params
#> TRACE [2025-08-22 07:30:56] All params
#> TRACE [2025-08-22 07:30:56] Small params
#> TRACE [2025-08-22 07:30:56] Advanced params
#> TRACE [2025-08-22 07:30:56] Changing params
#> TRACE [2025-08-22 07:30:56] Changing filenames
#> TRACE [2025-08-22 07:30:57] Exporting params
#> ✔ par_usr_cre_com completed [1.3s, 200 B]
#> + par_usr_pre_lib_sop_clo dispatched
#> TRACE [2025-08-22 07:30:57] Loading default params
#> TRACE [2025-08-22 07:30:57] All params
#> TRACE [2025-08-22 07:30:57] Small params
#> TRACE [2025-08-22 07:30:57] Advanced params
#> TRACE [2025-08-22 07:30:57] Changing params
#> TRACE [2025-08-22 07:30:57] Changing filenames
#> TRACE [2025-08-22 07:30:58] Exporting params
#> ✔ par_usr_pre_lib_sop_clo completed [1.3s, 205 B]
#> + par_usr_cre_edg_spe dispatched
#> TRACE [2025-08-22 07:30:59] Loading default params
#> TRACE [2025-08-22 07:30:59] All params
#> TRACE [2025-08-22 07:30:59] Small params
#> TRACE [2025-08-22 07:30:59] Advanced params
#> TRACE [2025-08-22 07:30:59] Changing params
#> TRACE [2025-08-22 07:30:59] Changing filenames
#> TRACE [2025-08-22 07:31:00] Exporting params
#> ✔ par_usr_cre_edg_spe completed [1.3s, 452 B]
#> + par_usr_pre_fea_com dispatched
#> TRACE [2025-08-22 07:31:00] Loading default params
#> TRACE [2025-08-22 07:31:00] All params
#> TRACE [2025-08-22 07:31:00] Small params
#> TRACE [2025-08-22 07:31:00] Advanced params
#> TRACE [2025-08-22 07:31:00] Changing params
#> TRACE [2025-08-22 07:31:00] Changing filenames
#> TRACE [2025-08-22 07:31:02] Exporting params
#> ✔ par_usr_pre_fea_com completed [1.5s, 200 B]
#> + par_usr_pre_fea_edg dispatched
#> TRACE [2025-08-22 07:31:02] Loading default params
#> TRACE [2025-08-22 07:31:02] All params
#> TRACE [2025-08-22 07:31:02] Small params
#> TRACE [2025-08-22 07:31:02] Advanced params
#> TRACE [2025-08-22 07:31:02] Changing params
#> TRACE [2025-08-22 07:31:02] Changing filenames
#> TRACE [2025-08-22 07:31:03] Exporting params
#> ✔ par_usr_pre_fea_edg completed [1.3s, 328 B]
#> + par_usr_pre_lib_sop_ecm dispatched
#> TRACE [2025-08-22 07:31:03] Loading default params
#> TRACE [2025-08-22 07:31:03] All params
#> TRACE [2025-08-22 07:31:03] Small params
#> TRACE [2025-08-22 07:31:03] Advanced params
#> TRACE [2025-08-22 07:31:03] Changing params
#> TRACE [2025-08-22 07:31:03] Changing filenames
#> TRACE [2025-08-22 07:31:05] Exporting params
#> ✔ par_usr_pre_lib_sop_ecm completed [1.3s, 176 B]
#> + par_usr_fil_ann dispatched
#> TRACE [2025-08-22 07:31:05] Loading default params
#> TRACE [2025-08-22 07:31:05] All params
#> TRACE [2025-08-22 07:31:05] Small params
#> TRACE [2025-08-22 07:31:05] Advanced params
#> TRACE [2025-08-22 07:31:05] Changing params
#> TRACE [2025-08-22 07:31:05] Changing filenames
#> TRACE [2025-08-22 07:31:06] Exporting params
#> ✔ par_usr_fil_ann completed [1.3s, 668 B]
#> + par_usr_pre_fea_tab dispatched
#> TRACE [2025-08-22 07:31:06] Loading default params
#> TRACE [2025-08-22 07:31:06] All params
#> TRACE [2025-08-22 07:31:06] Small params
#> TRACE [2025-08-22 07:31:06] Advanced params
#> TRACE [2025-08-22 07:31:06] Changing params
#> TRACE [2025-08-22 07:31:06] Changing filenames
#> TRACE [2025-08-22 07:31:08] Exporting params
#> ✔ par_usr_pre_fea_tab completed [1.3s, 274 B]
#> + par_usr_pre_lib_rt dispatched
#> TRACE [2025-08-22 07:31:08] Loading default params
#> TRACE [2025-08-22 07:31:08] All params
#> TRACE [2025-08-22 07:31:08] Small params
#> TRACE [2025-08-22 07:31:08] Advanced params
#> TRACE [2025-08-22 07:31:08] Changing params
#> TRACE [2025-08-22 07:31:08] Changing filenames
#> TRACE [2025-08-22 07:31:09] Exporting params
#> ✔ par_usr_pre_lib_rt completed [1.3s, 440 B]
#> + par_usr_ann_spe dispatched
#> TRACE [2025-08-22 07:31:09] Loading default params
#> TRACE [2025-08-22 07:31:09] All params
#> TRACE [2025-08-22 07:31:09] Small params
#> TRACE [2025-08-22 07:31:09] Advanced params
#> TRACE [2025-08-22 07:31:09] Changing params
#> TRACE [2025-08-22 07:31:09] Changing filenames
#> TRACE [2025-08-22 07:31:11] Exporting params
#> ✔ par_usr_ann_spe completed [1.3s, 1.03 kB]
#> + par_usr_pre_ann_spe dispatched
#> TRACE [2025-08-22 07:31:11] Loading default params
#> TRACE [2025-08-22 07:31:11] All params
#> TRACE [2025-08-22 07:31:11] Small params
#> TRACE [2025-08-22 07:31:11] Advanced params
#> TRACE [2025-08-22 07:31:11] Changing params
#> TRACE [2025-08-22 07:31:11] Changing filenames
#> TRACE [2025-08-22 07:31:12] Exporting params
#> ✔ par_usr_pre_ann_spe completed [1.3s, 731 B]
#> + par_usr_pre_lib_spe dispatched
#> TRACE [2025-08-22 07:31:12] Loading default params
#> TRACE [2025-08-22 07:31:12] All params
#> TRACE [2025-08-22 07:31:12] Small params
#> TRACE [2025-08-22 07:31:12] Advanced params
#> TRACE [2025-08-22 07:31:12] Changing params
#> TRACE [2025-08-22 07:31:12] Changing filenames
#> TRACE [2025-08-22 07:31:14] Exporting params
#> ✔ par_usr_pre_lib_spe completed [1.3s, 298 B]
#> + par_usr_pre_ann_sir dispatched
#> TRACE [2025-08-22 07:31:14] Loading default params
#> TRACE [2025-08-22 07:31:14] All params
#> TRACE [2025-08-22 07:31:14] Small params
#> TRACE [2025-08-22 07:31:14] Advanced params
#> TRACE [2025-08-22 07:31:14] Changing params
#> TRACE [2025-08-22 07:31:14] Changing filenames
#> TRACE [2025-08-22 07:31:15] Exporting params
#> ✔ par_usr_pre_ann_sir completed [1.3s, 900 B]
#> + par_usr_ann_mas dispatched
#> TRACE [2025-08-22 07:31:15] Loading default params
#> TRACE [2025-08-22 07:31:15] All params
#> TRACE [2025-08-22 07:31:15] Small params
#> TRACE [2025-08-22 07:31:15] Advanced params
#> TRACE [2025-08-22 07:31:15] Changing params
#> TRACE [2025-08-22 07:31:15] Changing filenames
#> TRACE [2025-08-22 07:31:17] Exporting params
#> ✔ par_usr_ann_mas completed [1.3s, 2.68 kB]
#> + par_usr_wei_ann dispatched
#> TRACE [2025-08-22 07:31:17] Loading default params
#> TRACE [2025-08-22 07:31:17] All params
#> TRACE [2025-08-22 07:31:17] Small params
#> TRACE [2025-08-22 07:31:17] Advanced params
#> TRACE [2025-08-22 07:31:17] Changing params
#> TRACE [2025-08-22 07:31:17] Changing filenames
#> TRACE [2025-08-22 07:31:18] Exporting params
#> ✔ par_usr_wei_ann completed [1.3s, 1.76 kB]
#> + par_pre_lib_sop_mer dispatched
#> ✔ par_pre_lib_sop_mer completed [1ms, 558 B]
#> + par_pre_lib_sop_lot dispatched
#> ✔ par_pre_lib_sop_lot completed [1ms, 186 B]
#> + par_pre_tax dispatched
#> ✔ par_pre_tax completed [1ms, 327 B]
#> + par_pre_ann_gnp dispatched
#> ✔ par_pre_ann_gnp completed [0ms, 336 B]
#> + par_pre_lib_sop_hmd dispatched
#> ✔ par_pre_lib_sop_hmd completed [1ms, 191 B]
#> + par_cre_com dispatched
#> ✔ par_cre_com completed [0ms, 191 B]
#> + par_pre_lib_sop_clo dispatched
#> ✔ par_pre_lib_sop_clo completed [0ms, 213 B]
#> + par_cre_edg_spe dispatched
#> ✔ par_cre_edg_spe completed [0ms, 389 B]
#> + par_pre_fea_com dispatched
#> ✔ par_pre_fea_com completed [0ms, 184 B]
#> + par_pre_fea_edg dispatched
#> ✔ par_pre_fea_edg completed [0ms, 244 B]
#> + par_pre_lib_sop_ecm dispatched
#> ✔ par_pre_lib_sop_ecm completed [1ms, 191 B]
#> + par_fil_ann dispatched
#> ✔ par_fil_ann completed [0ms, 347 B]
#> + par_pre_fea_tab dispatched
#> ✔ par_pre_fea_tab completed [1ms, 278 B]
#> + par_pre_lib_rt dispatched
#> ✔ par_pre_lib_rt completed [1ms, 329 B]
#> + par_ann_spe dispatched
#> ✔ par_ann_spe completed [1ms, 497 B]
#> + par_pre_ann_spe dispatched
#> ✔ par_pre_ann_spe completed [0ms, 334 B]
#> + par_pre_lib_spe dispatched
#> ✔ par_pre_lib_spe completed [1ms, 305 B]
#> + par_pre_ann_sir dispatched
#> ✔ par_pre_ann_sir completed [0ms, 405 B]
#> + par_ann_mas dispatched
#> ✔ par_ann_mas completed [1ms, 1.13 kB]
#> + par_wei_ann dispatched
#> ✔ par_wei_ann completed [1ms, 932 B]
#> + lib_sop_mer_str_pro dispatched
#> INFO [2025-08-22 07:31:22] Directory data/interim/libraries/sop/merged/structures created.
#> ✔ lib_sop_mer_str_pro completed [2.5s, 90.51 MB]
#> + lib_sop_lot_pre dispatched
#> TRACE [2025-08-22 07:31:24] Loading and preparing LOTUS
#> INFO [2025-08-22 07:31:35] ... path to export is data/interim/libraries/sop/lotus_prepared.tsv.gz
#> ✔ lib_sop_lot_pre completed [14.1s, 46.52 MB]
#> + lib_sop_hmd_pre dispatched
#> TRACE [2025-08-22 07:31:39] Unzipping HMDB
#> TRACE [2025-08-22 07:31:42] Loading HMDB
#> TRACE [2025-08-22 07:32:22] Formatting HMDB
#> TRACE [2025-08-22 07:32:23] Deleting unzipped file
#> INFO [2025-08-22 07:32:23] ... path to export is data/interim/libraries/sop/hmdb_prepared.tsv.gz
#> ✔ lib_sop_hmd_pre completed [44.7s, 8.06 MB]
#> + lib_sop_clo_pre dispatched
#> WARN [2025-08-22 07:32:24] Sorry, you do not have access to the closed resource,
#> returning an empty file instead
#> INFO [2025-08-22 07:32:24] Directory data/interim/params created.
#> INFO [2025-08-22 07:32:24] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:32:24] ... path to export is data/interim/libraries/sop/closed_prepared.tsv.gz
#> ✔ lib_sop_clo_pre completed [18ms, 273 B]
#> + lib_sop_ecm_pre dispatched
#> TRACE [2025-08-22 07:32:24] Loading ECMDB resources
#> TRACE [2025-08-22 07:32:25] Formatting ECMDB
#> INFO [2025-08-22 07:32:25] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:32:25] ... path to export is data/interim/libraries/sop/ecmdb_prepared.tsv.gz
#> ✔ lib_sop_ecm_pre completed [647ms, 177.47 kB]
#> + par_pre_fea_tab_fil_fea_raw dispatched
#> ✔ par_pre_fea_tab_fil_fea_raw completed [0ms, 451.55 kB]
#> + lib_rt dispatched
#> WARN [2025-08-22 07:32:25] No retention time library found, returning empty sop table.
#> WARN [2025-08-22 07:32:25] No retention time library found, returning empty retention time table.
#> INFO [2025-08-22 07:32:25] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:32:25] Directory data/interim/libraries/rt created.
#> INFO [2025-08-22 07:32:25] ... path to export is data/interim/libraries/rt/prepared.tsv.gz
#> INFO [2025-08-22 07:32:25] ... path to export is data/interim/libraries/sop/rt_prepared.tsv.gz
#> ✔ lib_rt completed [54ms, 182 B]
#> + par_ann_spe_fil_spe_raw dispatched
#> ✔ par_ann_spe_fil_spe_raw completed [0ms, 44.68 kB]
#> + lib_spe_exp_int_pre dispatched
#> TRACE [2025-08-22 07:32:26] Importing
#> TRACE [2025-08-22 07:32:27] Harmonizing names
#> TRACE [2025-08-22 07:32:27] Filtering MS2 only
#> TRACE [2025-08-22 07:32:27] Applying sanitization of the spectra
#> TRACE [2025-08-22 07:32:27] Filtering empty spectra
#> INFO [2025-08-22 07:32:27] Considering 402 spectra
#> TRACE [2025-08-22 07:32:27] Extracting
#> TRACE [2025-08-22 07:32:27] Harmonizing
#> TRACE [2025-08-22 07:32:27] ... pos
#> TRACE [2025-08-22 07:32:28] ... neg
#> TRACE [2025-08-22 07:32:28] Extracting structures for the SOP library.
#> INFO [2025-08-22 07:32:28] ... path to export is data/interim/libraries/sop/internal_prepared.tsv.gz
#> INFO [2025-08-22 07:32:28] ... path to used parameters is data/interim/params
#> ✔ lib_spe_exp_int_pre completed [1.8s, 155 B]
#> + input_features dispatched
#> ✔ input_features completed [1ms, 451.55 kB]
#> + lib_rt_sop dispatched
#> ✔ lib_rt_sop completed [0ms, 96 B]
#> + lib_rt_rts dispatched
#> ✔ lib_rt_rts completed [0ms, 86 B]
#> + input_spectra dispatched
#> INFO [2025-08-22 07:32:29] File already exists. Skipping.
#> ✔ input_spectra completed [1ms, 44.68 kB]
#> + lib_spe_exp_int_pre_sop dispatched
#> ✔ lib_spe_exp_int_pre_sop completed [0ms, 108 B]
#> + lib_spe_exp_int_pre_pos dispatched
#> ✔ lib_spe_exp_int_pre_pos completed [0ms, 139.71 kB]
#> + lib_spe_exp_int_pre_neg dispatched
#> ✔ lib_spe_exp_int_pre_neg completed [0ms, 50.68 kB]
#> + fea_pre dispatched
#> TRACE [2025-08-22 07:32:30] Preparing features table
#> TRACE [2025-08-22 07:32:30] Formatting feature table
#> TRACE [2025-08-22 07:32:30] ... requires 'Peak area' or ':area' in columns (mzmine format)
#> TRACE [2025-08-22 07:32:30] ... or 'quant_' in columns (SLAW format)
#> TRACE [2025-08-22 07:32:30] ... or 'Peak height' in columns (SIRIUS format)
#> TRACE [2025-08-22 07:32:30] Filtering top intensities per feature
#> INFO [2025-08-22 07:32:30] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:32:30] Directory data/interim/features created.
#> INFO [2025-08-22 07:32:30] ... path to export is data/interim/features/example_features.tsv.gz
#> ✔ fea_pre completed [149ms, 95.63 kB]
#> + fea_edg_spe dispatched
#> TRACE [2025-08-22 07:32:31] Harmonizing names
#> TRACE [2025-08-22 07:32:31] Filtering MS2 only
#> TRACE [2025-08-22 07:32:31] Combining spectra in case
#> TRACE [2025-08-22 07:32:32] Applying sanitization of the spectra
#> TRACE [2025-08-22 07:32:32] Filtering empty spectra
#> INFO [2025-08-22 07:32:32] Considering 22 spectra
#> TRACE [2025-08-22 07:32:32] Performing spectral comparison
#> TRACE [2025-08-22 07:32:32] As we do not limit the precursors delta,
#> expect a (relatively) long processing time.
#> INFO [2025-08-22 07:32:32] =====================================================
#> INFO [2025-08-22 07:32:32] = Take yourself a break, you deserve it.            =
#> INFO [2025-08-22 07:32:32] =====================================================
#> TRACE [2025-08-22 07:32:32] Calculating features' entropy
#> TRACE [2025-08-22 07:32:32] Counting features' number of peaks
#> INFO [2025-08-22 07:32:32] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:32:32] ... path to export is data/interim/features/example_edgesSpectra.tsv
#> ✔ fea_edg_spe completed [1.4s, 852 B]
#> + lib_sop_mer dispatched
#> TRACE [2025-08-22 07:32:32] Loading and concatenating prepared libraries
#> TRACE [2025-08-22 07:32:43] Splitting the concatenated library into smaller standardized pieces
#> TRACE [2025-08-22 07:32:51] Sanitizing structures
#> TRACE [2025-08-22 07:32:51] Processing SMILES
#> INFO [2025-08-22 07:33:01] Passing 61 SMILES to RDKit
#> [07:33:01] Explicit valence for atom # 1 N, 3, is greater than permitted
#> [07:33:01] ERROR: Could not sanitize molecule on line 1
#> [07:33:01] ERROR: Explicit valence for atom # 1 N, 3, is greater than permitted
#> [07:33:01] Explicit valence for atom # 0 P, 11, is greater than permitted
#> [07:33:01] ERROR: Could not sanitize molecule on line 2
#> [07:33:01] ERROR: Explicit valence for atom # 0 P, 11, is greater than permitted
#> [07:33:01] Explicit valence for atom # 21 N, 4, is greater than permitted
#> [07:33:01] ERROR: Could not sanitize molecule on line 3
#> [07:33:01] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
#> [07:33:01] Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [07:33:01] ERROR: Could not sanitize molecule on line 4
#> [07:33:01] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [07:33:01] Explicit valence for atom # 6 C, 5, is greater than permitted
#> [07:33:01] ERROR: Could not sanitize molecule on line 5
#> [07:33:01] ERROR: Explicit valence for atom # 6 C, 5, is greater than permitted
#> [07:33:01] Explicit valence for atom # 18 S, 7, is greater than permitted
#> [07:33:01] ERROR: Could not sanitize molecule on line 6
#> [07:33:01] ERROR: Explicit valence for atom # 18 S, 7, is greater than permitted
#> [07:33:01] SMILES Parse Error: syntax error while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [07:33:01] SMILES Parse Error: check for mistakes around position 76:
#> [07:33:01] C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C
#> [07:33:01] ~~~~~~~~~~~~~~~~~~~~^
#> [07:33:01] SMILES Parse Error: extra open parentheses while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [07:33:01] SMILES Parse Error: check for mistakes around position 32:
#> [07:33:01] C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2
#> [07:33:01] ~~~~~~~~~~~~~~~~~~~~^
#> [07:33:01] SMILES Parse Error: extra open parentheses while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [07:33:01] SMILES Parse Error: check for mistakes around position 49:
#> [07:33:01] )\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2
#> [07:33:01] ~~~~~~~~~~~~~~~~~~~~^
#> [07:33:01] SMILES Parse Error: extra open parentheses while parsing: OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1
#> [07:33:01] SMILES Parse Error: check for mistakes around position 66:
#> [07:33:01] )=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(
#> [07:33:01] ~~~~~~~~~~~~~~~~~~~~^
#> [07:33:01] SMILES Parse Error: Failed parsing SMILES 'OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1' for input: 'OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1'
#> [07:33:01] ERROR: Smiles parse error on line 7
#> [07:33:01] ERROR: Cannot create molecule from : 'OC1=CC=CC(=C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C1=CC(O)=CC=C1)\C1=CC(O)=CC=C1'
#> INFO [2025-08-22 07:33:23] Led to 877903 referenced structure-organism pairs
#> INFO [2025-08-22 07:33:27] Corresponding to 393389 unique stereoisomers (excluding structures without stereochemistry)...
#> INFO [2025-08-22 07:33:27] ... and 1007790 unique structures without stereochemistry...
#> INFO [2025-08-22 07:33:27] ... or 1184311 unique constitutional isomers (ignoring stereochemistry)
#> INFO [2025-08-22 07:33:48] ... among 36800 unique organisms
#> TRACE [2025-08-22 07:33:48] Keeping keys
#> TRACE [2025-08-22 07:33:48] Keeping organisms
#> TRACE [2025-08-22 07:33:48] Completing organisms taxonomy
#> TRACE [2025-08-22 07:33:48] Testing if Open Tree of Life API is up
#> TRACE [2025-08-22 07:33:48] Success! Submitting request
#> TRACE [2025-08-22 07:33:50] Request finished!
#> TRACE [2025-08-22 07:33:50] Getting taxonomy
#> TRACE [2025-08-22 07:33:50] Taxonomy retrieved!
#> TRACE [2025-08-22 07:33:50] Got OTTaxonomy!
#> TRACE [2025-08-22 07:33:50] Keeping structures
#> INFO [2025-08-22 07:33:50] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:33:50] ... path to export is data/interim/libraries/sop/merged/keys.tsv.gz
#> INFO [2025-08-22 07:33:51] Directory data/interim/libraries/sop/merged/organisms/taxonomies created.
#> INFO [2025-08-22 07:33:51] ... path to export is data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz
#> INFO [2025-08-22 07:33:51] ... path to export is data/interim/libraries/sop/merged/structures/stereo.tsv.gz
#> INFO [2025-08-22 07:33:55] ... path to export is data/interim/libraries/sop/merged/structures/metadata.tsv.gz
#> INFO [2025-08-22 07:33:56] ... path to export is data/interim/libraries/sop/merged/structures/names.tsv.gz
#> INFO [2025-08-22 07:33:57] Directory data/interim/libraries/sop/merged/structures/taxonomies created.
#> INFO [2025-08-22 07:33:57] ... path to export is data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz
#> INFO [2025-08-22 07:33:57] ... path to export is data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz
#> ✔ lib_sop_mer completed [1m 25.1s, 250 B]
#> + ann_spe_pos dispatched
#> TRACE [2025-08-22 07:33:58] Loading spectra
#> TRACE [2025-08-22 07:33:58] Harmonizing names
#> TRACE [2025-08-22 07:33:58] Filtering MS2 only
#> TRACE [2025-08-22 07:33:58] Combining spectra in case
#> TRACE [2025-08-22 07:33:59] Applying sanitization of the spectra
#> TRACE [2025-08-22 07:33:59] Filtering empty spectra
#> INFO [2025-08-22 07:33:59] Considering 22 spectra
#> TRACE [2025-08-22 07:33:59] Loading spectral libraries
#> TRACE [2025-08-22 07:34:14] Harmonizing spectrum id
#> TRACE [2025-08-22 07:34:14] Harmonizing spectrum id
#> TRACE [2025-08-22 07:34:23] Harmonizing spectrum id
#> TRACE [2025-08-22 07:34:23] Harmonizing spectrum id
#> TRACE [2025-08-22 07:34:28] Harmonizing spectrum id
#> INFO [2025-08-22 07:34:43] Annotating using following libraries
#> INFO [2025-08-22 07:34:45]          library spectra unique_connectivities
#>  ISDB - Wikidata  998198                998198
#>             gnps  354788                 22675
#>           merlin  208273                 26197
#>         massbank   66388                  5901
#>         internal     279                     1
#> TRACE [2025-08-22 07:34:46] Reducing library size
#> TRACE [2025-08-22 07:34:46] Annotating
#> TRACE [2025-08-22 07:34:48] Trying to harmonize adducts definitions
#> TRACE [2025-08-22 07:34:48] Filtering results above threshold only
#> INFO [2025-08-22 07:34:48] 5197 Candidates were annotated on 22 features, with at least 0 similarity score.
#> INFO [2025-08-22 07:34:48] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:34:48] ... path to export is data/interim/annotations/example_spectralMatches_pos.tsv.gz
#> ✔ ann_spe_pos completed [49.4s, 255.88 kB]
#> + ann_spe_neg dispatched
#> TRACE [2025-08-22 07:34:49] Loading spectra
#> TRACE [2025-08-22 07:34:49] Harmonizing names
#> TRACE [2025-08-22 07:34:49] Filtering MS2 only
#> TRACE [2025-08-22 07:34:49] Combining spectra in case
#> TRACE [2025-08-22 07:34:49] Applying sanitization of the spectra
#> TRACE [2025-08-22 07:34:49] Filtering empty spectra
#> INFO [2025-08-22 07:34:49] Considering 0 spectra
#> WARN [2025-08-22 07:34:49] No spectra matched the given polarity, returning an empty dataframe
#> INFO [2025-08-22 07:34:49] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:34:49] ... path to export is data/interim/annotations/example_spectralMatches_neg.tsv.gz
#> ✔ ann_spe_neg completed [219ms, 187 B]
#> + edg_spe dispatched
#> ✔ edg_spe completed [0ms, 852 B]
#> + lib_mer_key dispatched
#> ✔ lib_mer_key completed [0ms, 18.06 MB]
#> + lib_mer_str_met dispatched
#> ✔ lib_mer_str_met completed [1ms, 36.02 MB]
#> + lib_mer_str_nam dispatched
#> ✔ lib_mer_str_nam completed [0ms, 11.28 MB]
#> + lib_mer_str_stereo dispatched
#> ✔ lib_mer_str_stereo completed [1ms, 43.58 MB]
#> + lib_mer_str_tax_cla dispatched
#> ✔ lib_mer_str_tax_cla completed [0ms, 2.51 MB]
#> + lib_mer_str_tax_npc dispatched
#> ✔ lib_mer_str_tax_npc completed [0ms, 2.44 MB]
#> + lib_mer_org_tax_ott dispatched
#> ✔ lib_mer_org_tax_ott completed [0ms, 939.13 kB]
#> + ann_ms1_pre dispatched
#> TRACE [2025-08-22 07:35:11] Filtering desired adducts and adding mz tolerance
#> INFO [2025-08-22 07:35:11] Already 2112 adducts previously detected
#> TRACE [2025-08-22 07:35:11] Trying to harmonize adducts definitions
#> TRACE [2025-08-22 07:35:11] Calculating rt tolerance
#> TRACE [2025-08-22 07:35:11] Joining within given rt tolerance
#> INFO [2025-08-22 07:35:11] Here are the top 10 observed m/z differences inside the RT windows:
#> INFO [2025-08-22 07:35:11]              bin   N
#>  (4.8501,5.0366] 352
#>  (21.822,22.009] 283
#>   (16.973,17.16] 208
#>  (17.906,18.092] 192
#>  (15.854,16.041] 172
#>    (39.914,40.1] 143
#>  (38.981,39.168] 137
#>  (34.878,35.065] 115
#>  (77.962,78.148] 114
#>  (1.8659,2.0524] 108
#> INFO [2025-08-22 07:35:11] These differences may help identify potential preprocessing issues
#> TRACE [2025-08-22 07:35:11] Forming adducts and clusters
#> TRACE [2025-08-22 07:35:11] Calculating delta mz for single charge adducts and clusters
#> TRACE [2025-08-22 07:35:11] Joining within given delta mz tolerance (neutral losses)
#> TRACE [2025-08-22 07:35:11] Joining within given delta mz tolerance (adducts)
#> TRACE [2025-08-22 07:35:12] Keeping initial and destination feature
#> TRACE [2025-08-22 07:35:12] Joining with initial results (adducts)
#> TRACE [2025-08-22 07:35:12] Joining with initial results (neutral losses)
#> TRACE [2025-08-22 07:35:14] Joining within given mz tol to exact mass library
#> TRACE [2025-08-22 07:35:14] Keeping unique exact masses and molecular formulas
#> TRACE [2025-08-22 07:35:14] Joining exact masses with single charge adducts
#> TRACE [2025-08-22 07:35:14] Getting back to M
#> TRACE [2025-08-22 07:35:14] Calculating multicharged and in source dimers
#> TRACE [2025-08-22 07:35:42] Joining within given rt tolerance
#> TRACE [2025-08-22 07:35:42] Joining within given mz tol and filtering possible adducts
#> TRACE [2025-08-22 07:35:42] Joining single adducts, in source dimers, and multicharged
#> TRACE [2025-08-22 07:35:42] Adding chemical classification
#> INFO [2025-08-22 07:35:44] MS1 annotation led to 48099 annotations on 4224 features
#> INFO [2025-08-22 07:35:44] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:35:44] ... path to export is data/interim/features/example_edgesMasses.tsv
#> INFO [2025-08-22 07:35:44] ... path to export is data/interim/annotations/example_ms1Prepared.tsv.gz
#> ✔ ann_ms1_pre completed [51.9s, 158 B]
#> + ann_spe_exp_gnp_pre dispatched
#> WARN [2025-08-22 07:35:45] No GNPS annotations found, returning an empty file instead
#> INFO [2025-08-22 07:35:45] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:35:45] ... path to export is data/interim/annotations/example_gnpsPrepared.tsv.gz
#> ✔ ann_spe_exp_gnp_pre completed [22ms, 237 B]
#> + ann_spe_pre dispatched
#> TRACE [2025-08-22 07:35:46] Loading and formatting spectral matches
#> TRACE [2025-08-22 07:35:46] Selecting annotations columns
#> TRACE [2025-08-22 07:35:46] Trying to look for already computed metadata
#> TRACE [2025-08-22 07:35:48] Stereo loaded
#> TRACE [2025-08-22 07:35:53] Metadata loaded
#> TRACE [2025-08-22 07:36:01] Names loaded
#> TRACE [2025-08-22 07:36:01] Classyfire done
#> TRACE [2025-08-22 07:36:01] NPClassifier done
#> TRACE [2025-08-22 07:36:02] Metadata done
#> TRACE [2025-08-22 07:36:02] Names done
#> INFO [2025-08-22 07:36:06] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:06] ... path to export is data/interim/annotations/example_spectralMatchesPrepared.tsv.gz
#> ✔ ann_spe_pre completed [20.4s, 373.16 kB]
#> + ann_sir_pre dispatched
#> INFO [2025-08-22 07:36:07] Loading parameters for SIRIUS 6
#> TRACE [2025-08-22 07:36:07] Loading and formatting SIRIUS results...
#> TRACE [2025-08-22 07:36:07] ... CANOPUS loaded
#> TRACE [2025-08-22 07:36:07] ... formulas loaded
#> TRACE [2025-08-22 07:36:07] ... structures loaded
#> TRACE [2025-08-22 07:36:07] ... de novo loaded
#> TRACE [2025-08-22 07:36:07] ... CANOPUS prepared
#> TRACE [2025-08-22 07:36:07] ... formulas prepared
#> TRACE [2025-08-22 07:36:07] ... structures prepared
#> TRACE [2025-08-22 07:36:07] ... denovo prepared
#> TRACE [2025-08-22 07:36:07] Everything joined together
#> TRACE [2025-08-22 07:36:07] Selecting annotations columns
#> TRACE [2025-08-22 07:36:07] Trying to look for already computed metadata
#> TRACE [2025-08-22 07:36:10] Stereo loaded
#> TRACE [2025-08-22 07:36:17] Metadata loaded
#> TRACE [2025-08-22 07:36:24] Names loaded
#> TRACE [2025-08-22 07:36:25] Classyfire done
#> TRACE [2025-08-22 07:36:25] NPClassifier done
#> TRACE [2025-08-22 07:36:26] Metadata done
#> TRACE [2025-08-22 07:36:26] Names done
#> TRACE [2025-08-22 07:36:30] Splitting SIRIUS results
#> INFO [2025-08-22 07:36:30] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:30] ... path to export is data/interim/annotations/example_canopusPrepared.tsv.gz
#> INFO [2025-08-22 07:36:30] ... path to export is data/interim/annotations/example_formulaPrepared.tsv.gz
#> INFO [2025-08-22 07:36:30] ... path to export is data/interim/annotations/example_siriusPrepared.tsv.gz
#> ✔ ann_sir_pre completed [22.4s, 165 B]
#> + tax_pre dispatched
#> TRACE [2025-08-22 07:36:30] Loading feature table
#> TRACE [2025-08-22 07:36:30] Loading metadata table
#> TRACE [2025-08-22 07:36:30] Preparing organisms names
#> TRACE [2025-08-22 07:36:30] Retrieving already computed Open Tree of Life Taxonomy
#> TRACE [2025-08-22 07:36:30] Submitting the rest to OTL
#> TRACE [2025-08-22 07:36:30] Testing if Open Tree of Life API is up
#> TRACE [2025-08-22 07:36:31] Success! Submitting request
#> TRACE [2025-08-22 07:36:31] Request finished!
#> INFO [2025-08-22 07:36:31] Retrying with blk
#> TRACE [2025-08-22 07:36:31] Getting taxonomy
#> TRACE [2025-08-22 07:36:31] Taxonomy retrieved!
#> TRACE [2025-08-22 07:36:31] Got OTTaxonomy!
#> TRACE [2025-08-22 07:36:31] Joining all results
#> TRACE [2025-08-22 07:36:31] Joining with metadata table
#> TRACE [2025-08-22 07:36:31] Joining with cleaned taxonomy table
#> INFO [2025-08-22 07:36:31] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:31] Directory data/interim/taxa created.
#> INFO [2025-08-22 07:36:31] ... path to export is data/interim/taxa/example_taxed.tsv.gz
#> ✔ tax_pre completed [959ms, 19.70 kB]
#> + ann_ms1_pre_edg dispatched
#> ✔ ann_ms1_pre_edg completed [0ms, 81.71 kB]
#> + ann_ms1_pre_ann dispatched
#> ✔ ann_ms1_pre_ann completed [0ms, 10.81 MB]
#> + ann_sir_pre_can dispatched
#> ✔ ann_sir_pre_can completed [0ms, 784 B]
#> + ann_sir_pre_for dispatched
#> ✔ ann_sir_pre_for completed [0ms, 487 B]
#> + ann_sir_pre_str dispatched
#> ✔ ann_sir_pre_str completed [0ms, 24.42 kB]
#> + fea_edg_pre dispatched
#> TRACE [2025-08-22 07:36:33] Loading edge table
#> TRACE [2025-08-22 07:36:33] Formatting edge table
#> INFO [2025-08-22 07:36:34] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:34] ... path to export is data/interim/features/example_edges.tsv
#> ✔ fea_edg_pre completed [34ms, 93.83 kB]
#> + ann_fil dispatched
#> TRACE [2025-08-22 07:36:34] ... features
#> TRACE [2025-08-22 07:36:34] ... annotations
#> TRACE [2025-08-22 07:36:35] Removing MS1 annotations for which we have spectral hits
#> TRACE [2025-08-22 07:36:35] ... retention times
#> INFO [2025-08-22 07:36:35] Filtering annotations outside of Inf minutes tolerance
#> INFO [2025-08-22 07:36:35] 0 candidates were removed based on retention time.
#> INFO [2025-08-22 07:36:36] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:36] ... path to export is data/interim/annotations/example_annotationsFiltered.tsv.gz
#> ✔ ann_fil completed [2.5s, 11.66 MB]
#> + fea_com dispatched
#> INFO [2025-08-22 07:36:37] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:37] ... path to export is data/interim/features/example_components.tsv
#> ✔ fea_com completed [40ms, 24.13 kB]
#> + int_com dispatched
#> ✔ int_com completed [0ms, 24.13 kB]
#> + fea_com_pre dispatched
#> TRACE [2025-08-22 07:36:38] Loading files
#> TRACE [2025-08-22 07:36:38] Components table
#> INFO [2025-08-22 07:36:38] ... path to used parameters is data/interim/params
#> INFO [2025-08-22 07:36:38] ... path to export is data/interim/features/example_componentsPrepared.tsv
#> ✔ fea_com_pre completed [20ms, 24.12 kB]
#> + ann_pre dispatched
#> TRACE [2025-08-22 07:36:38] Loading files ...
#> TRACE [2025-08-22 07:36:38] ... components
#> TRACE [2025-08-22 07:36:38] ... edges
#> TRACE [2025-08-22 07:36:38] ... structure-organism pairs
#> TRACE [2025-08-22 07:36:48] ... canopus
#> TRACE [2025-08-22 07:36:48] ... formula
#> TRACE [2025-08-22 07:36:50] ... annotations
#> TRACE [2025-08-22 07:36:50] Initial annotations:
#> INFO [2025-08-22 07:36:50]  candidate_library      n
#>           TIMA MS1 161103
#>    ISDB - Wikidata   4867
#>             SIRIUS    479
#>             merlin    165
#>               gnps    151
#>           massbank     33
#> TRACE [2025-08-22 07:36:51] Re-arranging annotations
#> TRACE [2025-08-22 07:36:52] Adding biological organism metadata
#> TRACE [2025-08-22 07:36:53] Performing taxonomically informed scoring
#> TRACE [2025-08-22 07:36:55] Calculating biological score at all levels ...
#> TRACE [2025-08-22 07:36:55] ... domain
#> TRACE [2025-08-22 07:36:55] ... kingdom
#> TRACE [2025-08-22 07:36:55] ... phylum
#> TRACE [2025-08-22 07:36:55] ... class
#> TRACE [2025-08-22 07:36:55] ... order
#> TRACE [2025-08-22 07:36:55] ... family
#> TRACE [2025-08-22 07:36:55] ... tribe
#> TRACE [2025-08-22 07:36:55] ... genus
#> TRACE [2025-08-22 07:36:55] ... species
#> TRACE [2025-08-22 07:36:55] ... varietas
#> TRACE [2025-08-22 07:36:55] Keeping best biological score
#> INFO [2025-08-22 07:36:56] Taxonomically informed metabolite annotation led to 
#> 31600 annotations reranked at the kingdom level, 
#> 31342 annotations reranked at the phylum level, 
#> 26184 annotations reranked at the class level, 
#> 7506 annotations reranked at the order level, 
#> 6046 annotations reranked at the family level, 
#> 1020 annotations reranked at the tribe level, 
#> 812 annotations reranked at the genus level, 
#> 348 annotations reranked at the species level, and 
#> 0 annotations reranked at the variety level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! (for later predictions)
#> TRACE [2025-08-22 07:36:57] Calculating chemical consistency of features with at least 2 neighbors
#> TRACE [2025-08-22 07:36:57] Among all edges
#> TRACE [2025-08-22 07:36:57] ... at the (classyfire) kingdom level
#> TRACE [2025-08-22 07:36:57] ... at the (NPC) pathway level
#> TRACE [2025-08-22 07:36:57] ... at the (classyfire) superclass level
#> TRACE [2025-08-22 07:36:57] ... at the (NPC) superclass level
#> TRACE [2025-08-22 07:36:57] ... at the (classyfire) class level
#> TRACE [2025-08-22 07:36:57] ... at the (NPC) class level
#> TRACE [2025-08-22 07:36:57] ... at the (classyfire) parent level
#> TRACE [2025-08-22 07:36:58] Splitting already computed predictions
#> TRACE [2025-08-22 07:36:58] Joining all except -1 together
#> TRACE [2025-08-22 07:36:59] Adding already computed predictions back
#> TRACE [2025-08-22 07:37:00] Calculating chemical score at all levels ...
#> TRACE [2025-08-22 07:37:00] ... (classyfire) kingdom
#> TRACE [2025-08-22 07:37:00] ... (NPC) pathway
#> TRACE [2025-08-22 07:37:00] ... (classyfire) superclass
#> TRACE [2025-08-22 07:37:00] ... (NPC) superclass
#> TRACE [2025-08-22 07:37:00] ... (classyfire) class
#> TRACE [2025-08-22 07:37:00] ... (NPC) class
#> TRACE [2025-08-22 07:37:00] ... (classyfire) parent
#> TRACE [2025-08-22 07:37:00] ... keeping best chemical score
#> INFO [2025-08-22 07:37:01] Chemically informed scoring led to 
#> 13271 annotations reranked at the (classyfire) kingdom level, 
#> 9281 annotations reranked at the (NPC) pathway level, 
#> 7112 annotations reranked at the (classyfire) superclass level, 
#> 4758 annotations reranked at the (NPC) superclass level, 
#> 7112 annotations reranked at the (classyfire) class level, 
#> 4758 annotations reranked at the (NPC) class level, and 
#> 4747 annotations reranked at the (classyfire) parent level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!
#> INFO [2025-08-22 07:37:01] Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score 
#> TRACE [2025-08-22 07:37:08] Minimizing results
#> TRACE [2025-08-22 07:37:10] Keeping high confidence candidates only
#> INFO [2025-08-22 07:37:10] Removed 165909 low confidence candidates out of the 167725 total ones.
#> INFO [2025-08-22 07:37:10] 1816 high confidence candidates remaining.
#> TRACE [2025-08-22 07:37:10] Processing full results
#> TRACE [2025-08-22 07:37:10] Adding initial metadata (RT, etc.) and simplifying columns
#> TRACE [2025-08-22 07:37:15] Selecting columns to export
#> TRACE [2025-08-22 07:37:15] Adding consensus again to droped candidates
#> TRACE [2025-08-22 07:37:16] Processing filtered results
#> TRACE [2025-08-22 07:37:16] Adding initial metadata (RT, etc.) and simplifying columns
#> TRACE [2025-08-22 07:37:21] Selecting columns to export
#> TRACE [2025-08-22 07:37:21] Adding consensus again to droped candidates
#> INFO [2025-08-22 07:37:23] Directory data/processed/20250822_073723_example created.
#> INFO [2025-08-22 07:37:23] ... path to used parameters is data/processed/20250822_073723_example
#> INFO [2025-08-22 07:37:23] ... path to used parameters is data/processed/20250822_073723_example
#> INFO [2025-08-22 07:37:23] ... path to export is data/processed/20250822_073723_example/example_results_mini.tsv
#> INFO [2025-08-22 07:37:23] ... path to export is data/processed/20250822_073723_example/example_results_filtered.tsv
#> INFO [2025-08-22 07:37:23] ... path to export is data/processed/20250822_073723_example/example_results.tsv
#> ✔ ann_pre completed [45s, 3.76 MB]
#> ✔ ended pipeline [10m 34.1s, 126 completed, 0 skipped]
#> There were 15 warnings (use warnings() to see them)
#> Processing complete. Total molecules processed: 54
#> [1] TRUE

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Citation

BibTeX citation:

@online{rutz2025,
  author = {Rutz, Adriano},
  title = {3 {Performing} {Taxonomically} {Informed} {Metabolite}
    {Annotation}},
  date = {2025-08-22},
  url = {https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/III-processing.html},
  langid = {en}
}

For attribution, please cite this work as:

Rutz, Adriano. 2025. “3 Performing Taxonomically Informed Metabolite Annotation.” August 22, 2025. https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/III-processing.html.