3 Performing Taxonomically Informed Metabolite Annotation

Author

Adriano Rutz

Published

December 11, 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::run_tima()
#> + par_def_pre_lib_sop_ecm dispatched
#> ✔ par_def_pre_lib_sop_ecm completed [28ms, 492 B]
#> + par_def_ann_mas dispatched
#> ✔ par_def_ann_mas completed [1ms, 6.09 kB]
#> + par_def_pre_ann_spe dispatched
#> ✔ par_def_pre_ann_spe completed [1ms, 1.46 kB]
#> + par_def_fil_ann dispatched
#> ✔ par_def_fil_ann completed [1ms, 1.34 kB]
#> + par_def_cre_edg_spe dispatched
#> ✔ par_def_cre_edg_spe completed [0ms, 1.42 kB]
#> + par_def_pre_lib_sop_lot dispatched
#> ✔ par_def_pre_lib_sop_lot completed [1ms, 494 B]
#> + par_def_pre_ann_sir dispatched
#> ✔ par_def_pre_ann_sir completed [1ms, 1.93 kB]
#> + par_def_pre_lib_sop_mer dispatched
#> ✔ par_def_pre_lib_sop_mer completed [1ms, 3.39 kB]
#> + par_def_pre_lib_sop_big dispatched
#> ✔ par_def_pre_lib_sop_big completed [1ms, 314 B]
#> + par_def_ann_spe dispatched
#> ✔ par_def_ann_spe completed [0ms, 2.14 kB]
#> + par_def_pre_fea_com dispatched
#> ✔ par_def_pre_fea_com completed [1ms, 358 B]
#> + par_def_pre_tax dispatched
#> ✔ par_def_pre_tax completed [0ms, 1.51 kB]
#> + par_def_pre_lib_sop_hmd dispatched
#> ✔ par_def_pre_lib_sop_hmd completed [1ms, 492 B]
#> + par_def_pre_fea_edg dispatched
#> ✔ par_def_pre_fea_edg completed [1ms, 706 B]
#> + par_def_pre_fea_tab dispatched
#> ✔ par_def_pre_fea_tab completed [0ms, 860 B]
#> + par_def_pre_ann_gnp dispatched
#> ✔ par_def_pre_ann_gnp completed [1ms, 1.42 kB]
#> + par_def_pre_lib_spe dispatched
#> ✔ par_def_pre_lib_spe completed [1ms, 1.57 kB]
#> + par_def_pre_lib_rt dispatched
#> ✔ par_def_pre_lib_rt completed [1ms, 2.20 kB]
#> + par_def_wei_ann dispatched
#> ✔ par_def_wei_ann completed [1ms, 5.34 kB]
#> + par_def_pre_lib_sop_clo dispatched
#> ✔ par_def_pre_lib_sop_clo completed [1ms, 523 B]
#> + par_def_cre_com dispatched
#> ✔ par_def_cre_com completed [1ms, 375 B]
#> + yaml_paths dispatched
#> ✔ yaml_paths completed [1ms, 11.70 kB]
#> + paths dispatched
#> ✔ paths completed [1ms, 2.55 kB]
#> + lib_spe_exp_mer_pre_pos dispatched
#> [2025-12-11 19:11:17.511] [INFO ] Downloaded: merlin_13911806_pos.rds (81 MB)
#> ✔ lib_spe_exp_mer_pre_pos completed [589ms, 84.94 MB]
#> + lib_spe_exp_mer_pre_neg dispatched
#> [2025-12-11 19:11:17.946] [INFO ] Downloaded: merlin_13911806_neg.rds (30.1 MB)
#> ✔ lib_spe_exp_mer_pre_neg completed [232ms, 31.54 MB]
#> + lib_spe_exp_gnp_pre_pos dispatched
#> [2025-12-11 19:11:19.938] [INFO ] Downloaded: gnps_11566051_pos.rds (459 MB)
#> ✔ lib_spe_exp_gnp_pre_pos completed [1.8s, 481.27 MB]
#> + lib_spe_exp_mb_pre_pos dispatched
#> [2025-12-11 19:11:20.445] [INFO ] Downloaded: massbank_2025051_pos.rds (18.5 MB)
#> ✔ lib_spe_exp_mb_pre_pos completed [159ms, 19.41 MB]
#> + lib_spe_is_wik_pre_pos dispatched
#> Downloading  30% ■■■■■■■■■■                        2s
#> Downloading  75% ■■■■■■■■■■■■■■■■■■■■■■■■          1s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> [2025-12-11 19:11:23.942] [INFO ] Downloaded: wikidata_5607185_pos.rds (823.9 MB)
#> ✔ lib_spe_is_wik_pre_pos completed [3.3s, 863.95 MB]
#> + par_pre_par dispatched
#> ✔ par_pre_par completed [0ms, 1.38 kB]
#> + par_pre_par2 dispatched
#> ✔ par_pre_par2 completed [0ms, 21.68 kB]
#> + lib_sop_hmd dispatched
#> Downloading  45% ■■■■■■■■■■■■■■                    2s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> [2025-12-11 19:11:28.273] [INFO ] Downloaded: structures.zip (92 MB)
#> ✔ lib_sop_hmd completed [3.5s, 96.48 MB]
#> + lib_sop_ecm dispatched
#> [2025-12-11 19:11:29.579] [INFO ] Downloaded: ecmdb.json.zip (1.3 MB)
#> ✔ lib_sop_ecm completed [1.1s, 1.33 MB]
#> + lib_spe_exp_mer_pre_sop dispatched
#> [2025-12-11 19:11:29.991] [INFO ] Downloaded: merlin_13911806_prepared.tsv.gz (1.1 MB)
#> ✔ lib_spe_exp_mer_pre_sop completed [238ms, 1.19 MB]
#> + lib_sop_lot dispatched
#> [2025-12-11 19:11:30.162] [INFO ] Retrieving latest version from Zenodo: 10.5281/zenodo.5794106
#> [2025-12-11 19:11:32.005] [INFO ] Downloading 230106_frozen_metadata.csv.gz from https://doi.org/10.5281/zenodo.5794106
#> [2025-12-11 19:11:36.172] [INFO ] Downloaded: lotus.csv.gz (88.7 MB)
#> [2025-12-11 19:11:36.174] [INFO ] Download completed: data/source/libraries/sop/lotus.csv.gz
#> ✔ lib_sop_lot completed [6s, 92.98 MB]
#> + lib_spe_is_wik_pre_neg dispatched
#> Downloading  39% ■■■■■■■■■■■■■                     2s
#> Downloading  80% ■■■■■■■■■■■■■■■■■■■■■■■■■         0s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> [2025-12-11 19:11:38.991] [INFO ] Downloaded: wikidata_5607185_neg.rds (655.5 MB)
#> ✔ lib_spe_is_wik_pre_neg completed [2.6s, 687.33 MB]
#> + lib_spe_exp_mb_pre_sop dispatched
#> [2025-12-11 19:11:39.503] [INFO ] Downloaded: massbank_2025051_prepared.tsv.gz (469.7 KB)
#> ✔ lib_spe_exp_mb_pre_sop completed [104ms, 480.97 kB]
#> + lib_spe_exp_gnp_pre_sop dispatched
#> [2025-12-11 19:11:39.841] [INFO ] Downloaded: gnps_11566051_prepared.tsv.gz (1.4 MB)
#> ✔ lib_spe_exp_gnp_pre_sop completed [170ms, 1.42 MB]
#> + lib_spe_is_wik_pre_sop dispatched
#> [2025-12-11 19:11:40.261] [INFO ] Downloaded: wikidata_5607185_prepared.tsv.gz (36.1 MB)
#> ✔ lib_spe_is_wik_pre_sop completed [253ms, 37.90 MB]
#> + lib_spe_exp_gnp_pre_neg dispatched
#> [2025-12-11 19:11:41.062] [INFO ] Downloaded: gnps_11566051_neg.rds (147 MB)
#> ✔ lib_spe_exp_gnp_pre_neg completed [624ms, 154.12 MB]
#> + lib_spe_exp_mb_pre_neg dispatched
#> [2025-12-11 19:11:41.413] [INFO ] Downloaded: massbank_2025051_neg.rds (6.7 MB)
#> ✔ lib_spe_exp_mb_pre_neg completed [119ms, 7.06 MB]
#> + par_fin_par dispatched
#> ✔ par_fin_par completed [0ms, 307 B]
#> + par_fin_par2 dispatched
#> ✔ par_fin_par2 completed [2ms, 3.02 kB]
#> + par_usr_pre_ann_spe dispatched
#> ✔ par_usr_pre_ann_spe completed [1.6s, 731 B]
#> + par_usr_ann_spe dispatched
#> ✔ par_usr_ann_spe completed [1.5s, 1.03 kB]
#> + par_usr_wei_ann dispatched
#> ✔ par_usr_wei_ann completed [1.5s, 1.80 kB]
#> + par_usr_pre_lib_sop_ecm dispatched
#> ✔ par_usr_pre_lib_sop_ecm completed [1.5s, 176 B]
#> + par_usr_ann_mas dispatched
#> ✔ par_usr_ann_mas completed [1.5s, 2.68 kB]
#> + par_usr_pre_fea_edg dispatched
#> ✔ par_usr_pre_fea_edg completed [1.5s, 328 B]
#> + par_usr_fil_ann dispatched
#> ✔ par_usr_fil_ann completed [1.5s, 668 B]
#> + par_usr_pre_lib_sop_lot dispatched
#> ✔ par_usr_pre_lib_sop_lot completed [1.5s, 174 B]
#> + par_usr_pre_ann_sir dispatched
#> ✔ par_usr_pre_ann_sir completed [1.6s, 900 B]
#> + par_usr_pre_lib_spe dispatched
#> ✔ par_usr_pre_lib_spe completed [1.5s, 298 B]
#> + par_usr_pre_lib_sop_mer dispatched
#> ✔ par_usr_pre_lib_sop_mer completed [1.5s, 1.60 kB]
#> + par_usr_pre_fea_com dispatched
#> ✔ par_usr_pre_fea_com completed [1.5s, 200 B]
#> + par_usr_pre_lib_sop_big dispatched
#> ✔ par_usr_pre_lib_sop_big completed [1.5s, 107 B]
#> + par_usr_pre_ann_gnp dispatched
#> ✔ par_usr_pre_ann_gnp completed [1.5s, 708 B]
#> + par_usr_cre_com dispatched
#> ✔ par_usr_cre_com completed [1.5s, 200 B]
#> + par_usr_pre_lib_sop_hmd dispatched
#> ✔ par_usr_pre_lib_sop_hmd completed [1.5s, 178 B]
#> + par_usr_cre_edg_spe dispatched
#> ✔ par_usr_cre_edg_spe completed [1.5s, 452 B]
#> + par_usr_pre_fea_tab dispatched
#> ✔ par_usr_pre_fea_tab completed [1.5s, 274 B]
#> + par_usr_pre_lib_rt dispatched
#> ✔ par_usr_pre_lib_rt completed [1.5s, 487 B]
#> + par_usr_pre_lib_sop_clo dispatched
#> ✔ par_usr_pre_lib_sop_clo completed [1.5s, 267 B]
#> + par_usr_pre_tax dispatched
#> ✔ par_usr_pre_tax completed [1.5s, 438 B]
#> + par_pre_ann_spe dispatched
#> ✔ par_pre_ann_spe completed [1ms, 334 B]
#> + par_ann_spe dispatched
#> ✔ par_ann_spe completed [2ms, 497 B]
#> + par_wei_ann dispatched
#> ✔ par_wei_ann completed [2ms, 967 B]
#> + par_pre_lib_sop_ecm dispatched
#> ✔ par_pre_lib_sop_ecm completed [1ms, 191 B]
#> + par_ann_mas dispatched
#> ✔ par_ann_mas completed [2ms, 1.13 kB]
#> + par_pre_fea_edg dispatched
#> ✔ par_pre_fea_edg completed [1ms, 244 B]
#> + par_fil_ann dispatched
#> ✔ par_fil_ann completed [1ms, 346 B]
#> + par_pre_lib_sop_lot dispatched
#> ✔ par_pre_lib_sop_lot completed [2ms, 186 B]
#> + par_pre_ann_sir dispatched
#> ✔ par_pre_ann_sir completed [2ms, 405 B]
#> + par_pre_lib_spe dispatched
#> ✔ par_pre_lib_spe completed [1ms, 404 B]
#> + par_pre_lib_sop_mer dispatched
#> ✔ par_pre_lib_sop_mer completed [1ms, 559 B]
#> + par_pre_fea_com dispatched
#> ✔ par_pre_fea_com completed [1ms, 184 B]
#> + par_pre_lib_sop_big dispatched
#> ✔ par_pre_lib_sop_big completed [1ms, 155 B]
#> + par_pre_ann_gnp dispatched
#> ✔ par_pre_ann_gnp completed [1ms, 336 B]
#> + par_cre_com dispatched
#> ✔ par_cre_com completed [1ms, 191 B]
#> + par_pre_lib_sop_hmd dispatched
#> ✔ par_pre_lib_sop_hmd completed [1ms, 191 B]
#> + par_cre_edg_spe dispatched
#> ✔ par_cre_edg_spe completed [2ms, 389 B]
#> + par_pre_fea_tab dispatched
#> ✔ par_pre_fea_tab completed [2ms, 278 B]
#> + par_pre_lib_rt dispatched
#> ✔ par_pre_lib_rt completed [2ms, 375 B]
#> + par_pre_lib_sop_clo dispatched
#> ✔ par_pre_lib_sop_clo completed [1ms, 232 B]
#> + par_pre_tax dispatched
#> ✔ par_pre_tax completed [1ms, 330 B]
#> + par_ann_spe_fil_spe_raw dispatched
#> ✔ par_ann_spe_fil_spe_raw completed [0ms, 7.77 MB]
#> + lib_sop_ecm_pre dispatched
#> [2025-12-11 19:12:20.992] [INFO ] Preparing ECMDB structure-organism pairs
#> [2025-12-11 19:12:21.670] [INFO ] Exporting parameters to: data/interim/params/251211_191221_prepare_libraries_sop_ecmdb.yaml
#> [2025-12-11 19:12:21.688] [INFO ] Exported: ecmdb_prepared.tsv.gz (3,760 rows, 173.3 KB)
#> ✔ lib_sop_ecm_pre completed [699ms, 177.47 kB]
#> + lib_sop_lot_pre dispatched
#> [2025-12-11 19:12:21.881] [INFO ] Loading LOTUS database: lotus.csv.gz (88.7 MB)
#> [2025-12-11 19:12:33.445] [INFO ] Prepared unique structure-organism pairs from LOTUS (791,809)
#> [2025-12-11 19:12:36.999] [INFO ] Exported: lotus_prepared.tsv.gz (791,809 rows, 44.4 MB)
#> ✔ lib_sop_lot_pre completed [15.1s, 46.52 MB]
#> + lib_spe_exp_int_pre dispatched
#> [2025-12-11 19:12:37.400] [INFO ] Preparing spectral library: internal
#> [2025-12-11 19:12:37.405] [WARN ] Input file(s) not found; creating empty library template
#> [2025-12-11 19:12:38.746] [INFO ] Exporting spectral library files
#> [2025-12-11 19:12:38.752] [INFO ] Exported: internal_prepared.tsv.gz (1 rows, 106 B)
#> [2025-12-11 19:12:38.820] [INFO ] Exporting parameters to: data/interim/params/251211_191238_prepare_libraries_spectra.yaml
#> [2025-12-11 19:12:38.822] [INFO ] Spectral library 'internal' prepared successfully
#> ✔ lib_spe_exp_int_pre completed [1.4s, 1.30 kB]
#> + lib_sop_mer_str_pro dispatched
#> [2025-12-11 19:12:39.696] [INFO ] Downloaded: processed.csv.gz (86.3 MB)
#> ✔ lib_sop_mer_str_pro completed [480ms, 90.51 MB]
#> + lib_sop_big_pre dispatched
#> [2025-12-11 19:12:40.046] [INFO ] Preparing BiGG structure-organism pairs
#> [2025-12-11 19:13:04.060] [INFO ] Processing SMILES with RDKit
#> [2025-12-11 19:13:05.297] [INFO ] Processing 1416 new SMILES with RDKit
#> 2025-12-11 19:13:05,299 - __main__ - INFO - Starting SMILES processing pipeline
#> 2025-12-11 19:13:05,299 - __main__ - INFO - Input: /tmp/RtmpraLwtt/file21265652d207.smi
#> 2025-12-11 19:13:05,299 - __main__ - INFO - Output: /tmp/RtmpraLwtt/file21267078ae7c.csv.gz
#> 2025-12-11 19:13:05,299 - __main__ - INFO - Input file validated: /tmp/RtmpraLwtt/file21265652d207.smi
#> 2025-12-11 19:13:05,299 - __main__ - INFO - Output file validated: /tmp/RtmpraLwtt/file21267078ae7c.csv.gz
#> 2025-12-11 19:13:05,299 - __main__ - INFO - Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> 2025-12-11 19:13:05,300 - __main__ - INFO - SMILES supplier initialized
#> 2025-12-11 19:13:11,307 - __main__ - INFO - Processing complete. Total molecules processed: 1416
#> [2025-12-11 19:13:11.346] [INFO ] Successfully processed 1416 SMILES
#> [2025-12-11 19:13:19.175] [INFO ] Processing SMILES with RDKit
#> [2025-12-11 19:13:19.188] [INFO ] Processing 1229 new SMILES with RDKit
#> 2025-12-11 19:13:19,190 - __main__ - INFO - Starting SMILES processing pipeline
#> 2025-12-11 19:13:19,190 - __main__ - INFO - Input: /tmp/RtmpraLwtt/file21266917a743.smi
#> 2025-12-11 19:13:19,190 - __main__ - INFO - Output: /tmp/RtmpraLwtt/file212666633c9a.csv.gz
#> 2025-12-11 19:13:19,190 - __main__ - INFO - Input file validated: /tmp/RtmpraLwtt/file21266917a743.smi
#> 2025-12-11 19:13:19,190 - __main__ - INFO - Output file validated: /tmp/RtmpraLwtt/file212666633c9a.csv.gz
#> 2025-12-11 19:13:19,190 - __main__ - INFO - Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> 2025-12-11 19:13:19,190 - __main__ - INFO - SMILES supplier initialized
#> 2025-12-11 19:13:24,352 - __main__ - INFO - Processing complete. Total molecules processed: 1229
#> [2025-12-11 19:13:24.387] [INFO ] Successfully processed 1229 SMILES
#> [2025-12-11 19:13:24.482] [INFO ] Exported: bigg_prepared.tsv.gz (2,352 rows, 83.2 KB)
#> ✔ lib_sop_big_pre completed [44.4s, 85.19 kB]
#> + lib_sop_hmd_pre dispatched
#> [2025-12-11 19:13:24.869] [INFO ] Preparing HMDB structure-organism pairs
#> [2025-12-11 19:14:12.662] [INFO ] Exported: hmdb_prepared.tsv.gz (217,776 rows, 7.7 MB)
#> ✔ lib_sop_hmd_pre completed [47.8s, 8.06 MB]
#> + par_pre_fea_tab_fil_fea_raw dispatched
#> ✔ par_pre_fea_tab_fil_fea_raw completed [1ms, 451.55 kB]
#> + lib_rt dispatched
#> [2025-12-11 19:14:13.792] [INFO ] Preparing retention time libraries
#> [2025-12-11 19:14:13.804] [WARN ] No retention time library found, returning empty retention time and sop tables.
#> [2025-12-11 19:14:13.848] [INFO ] Exporting parameters to: data/interim/params/251211_191413_prepare_libraries_rt.yaml
#> [2025-12-11 19:14:13.850] [INFO ] Exported: prepared.tsv.gz (1 rows, 86 B)
#> [2025-12-11 19:14:13.853] [INFO ] Exported: rt_prepared.tsv.gz (1 rows, 105 B)
#> ✔ lib_rt completed [64ms, 191 B]
#> + lib_sop_clo_pre dispatched
#> [2025-12-11 19:14:14.217] [INFO ] Preparing closed structure-organism pairs library
#> [2025-12-11 19:14:14.218] [WARN ] Closed resource not accessible at: ~/Git/lotus-processor/data/processed/240412_closed_metadata.csv.gz. Returning empty template instead.
#> [2025-12-11 19:14:14.234] [INFO ] Exporting parameters to: data/interim/params/251211_191414_prepare_libraries_sop_closed.yaml
#> [2025-12-11 19:14:14.237] [INFO ] Exported: closed_prepared.tsv.gz (1 rows, 273 B)
#> ✔ lib_sop_clo_pre completed [21ms, 273 B]
#> + input_spectra dispatched
#> ✔ input_spectra completed [0ms, 7.77 MB]
#> + lib_spe_exp_int_pre_sop dispatched
#> ✔ lib_spe_exp_int_pre_sop completed [0ms, 106 B]
#> + lib_spe_exp_int_pre_pos dispatched
#> ✔ lib_spe_exp_int_pre_pos completed [0ms, 599 B]
#> + lib_spe_exp_int_pre_neg dispatched
#> ✔ lib_spe_exp_int_pre_neg completed [0ms, 599 B]
#> + input_features dispatched
#> ✔ input_features completed [0ms, 451.55 kB]
#> + lib_rt_sop dispatched
#> ✔ lib_rt_sop completed [0ms, 105 B]
#> + lib_rt_rts dispatched
#> ✔ lib_rt_rts completed [0ms, 86 B]
#> + fea_edg_spe dispatched
#> [2025-12-11 19:14:17.147] [INFO ] Creating spectral similarity network edges
#> [2025-12-11 19:14:17.149] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-12-11 19:14:17.175] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-12-11 19:14:18.872] [INFO ] Processed 10000 spectra...
#> [2025-12-11 19:14:20.109] [INFO ] Total spectra read: 16282
#> [2025-12-11 19:14:25.940] [INFO ] Loaded 16282 spectra from file
#> [2025-12-11 19:14:28.431] [INFO ] Sanitizing 4087 spectra (cutoff: 0)
#> [2025-12-11 19:14:29.324] [INFO ] Sanitization complete: 3331/4087 spectra retained (81.5%, 756 removed)
#> [2025-12-11 19:14:29.325] [INFO ] Import complete: 3331 spectra ready for analysis
#> [2025-12-11 19:14:29.326] [INFO ] ======================================
#> [2025-12-11 19:14:29.327] [INFO ] Take yourself a break, you deserve it.
#> [2025-12-11 19:14:29.328] [INFO ] ======================================
#> [2025-12-11 19:18:33.996] [INFO ] Created 7265 edges passing thresholds
#> [2025-12-11 19:18:34.063] [INFO ] Exporting parameters to: data/interim/params/251211_191834_create_edges_spectra.yaml
#> [2025-12-11 19:18:34.067] [INFO ] Exported: example_edgesSpectra.tsv (9,237 rows, 427.6 KB)
#> ✔ fea_edg_spe completed [4m 16.9s, 437.86 kB]
#> + ann_spe_pos dispatched
#> [2025-12-11 19:18:34.539] [INFO ] Starting spectral annotation in pos mode
#> [2025-12-11 19:18:34.540] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-12-11 19:18:34.541] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-12-11 19:18:36.255] [INFO ] Processed 10000 spectra...
#> [2025-12-11 19:18:37.487] [INFO ] Total spectra read: 16282
#> [2025-12-11 19:18:43.275] [INFO ] Loaded 16282 spectra from file
#> [2025-12-11 19:18:44.099] [INFO ] Sanitizing 4087 spectra (cutoff: 0)
#> [2025-12-11 19:18:45.069] [INFO ] Sanitization complete: 3331/4087 spectra retained (81.5%, 756 removed)
#> [2025-12-11 19:18:45.070] [INFO ] Import complete: 3331 spectra ready for analysis
#> [2025-12-11 19:18:45.072] [INFO ] Importing spectra from: data/interim/libraries/spectra/is/wikidata_5607185_pos.rds
#> [2025-12-11 19:19:07.913] [INFO ] Loaded 998198 spectra from file
#> [2025-12-11 19:19:08.596] [INFO ] Import complete: 998198 spectra ready for analysis
#> [2025-12-11 19:19:08.597] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/internal_pos.rds
#> [2025-12-11 19:19:08.598] [INFO ] Loaded 1 spectra from file
#> [2025-12-11 19:19:08.600] [INFO ] Import complete: 0 spectra ready for analysis
#> [2025-12-11 19:19:08.601] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/gnps_11566051_pos.rds
#> [2025-12-11 19:19:16.276] [INFO ] Loaded 354789 spectra from file
#> [2025-12-11 19:19:16.496] [INFO ] Import complete: 354788 spectra ready for analysis
#> [2025-12-11 19:19:16.498] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/massbank_2025051_pos.rds
#> [2025-12-11 19:19:17.236] [INFO ] Loaded 66388 spectra from file
#> [2025-12-11 19:19:17.280] [INFO ] Import complete: 66388 spectra ready for analysis
#> [2025-12-11 19:19:17.282] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/merlin_13911806_pos.rds
#> [2025-12-11 19:19:22.138] [INFO ] Loaded 208280 spectra from file
#> [2025-12-11 19:19:22.307] [INFO ] Import complete: 208273 spectra ready for analysis
#> [2025-12-11 19:19:36.024] [INFO ] 
#>          library spectra unique_connectivities
#>  ISDB - Wikidata  998198                998198
#>             gnps  354788                 22675
#>           merlin  208273                 26197
#>         massbank   66388                  5901
#> [2025-12-11 19:19:37.315] [INFO ] Calculating entropy and similarity for 3331 spectra
#> [2025-12-11 19:24:14.619] [INFO ] 298156 Candidates annotated on 3175 features (threshold >= 0).
#> [2025-12-11 19:24:14.622] [INFO ] Exporting parameters to: data/interim/params/251211_192414_annotate_spectra.yaml
#> [2025-12-11 19:24:16.197] [INFO ] Exported: example_spectralMatches_pos.tsv.gz (568,675 rows, 31.7 MB)
#> ✔ ann_spe_pos completed [5m 41.7s, 33.24 MB]
#> + ann_spe_neg dispatched
#> [2025-12-11 19:24:17.922] [INFO ] Starting spectral annotation in neg mode
#> [2025-12-11 19:24:17.923] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-12-11 19:24:17.924] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-12-11 19:24:19.597] [INFO ] Processed 10000 spectra...
#> [2025-12-11 19:24:20.892] [INFO ] Total spectra read: 16282
#> [2025-12-11 19:24:26.149] [INFO ] Loaded 16282 spectra from file
#> [2025-12-11 19:24:26.163] [WARN ] No spectra to sanitize
#> [2025-12-11 19:24:26.164] [INFO ] Import complete: 0 spectra ready for analysis
#> [2025-12-11 19:24:26.165] [WARN ] No query spectra loaded
#> [2025-12-11 19:24:26.168] [INFO ] Exporting parameters to: data/interim/params/251211_192426_annotate_spectra.yaml
#> [2025-12-11 19:24:26.169] [WARN ] Returning empty annotation template
#> [2025-12-11 19:24:26.258] [INFO ] Exported: example_spectralMatches_neg.tsv.gz (1 rows, 237 B)
#> ✔ ann_spe_neg completed [8.5s, 237 B]
#> + fea_pre dispatched
#> [2025-12-11 19:24:27.071] [INFO ] Preparing features table from: data/source/example_features.csv
#> [2025-12-11 19:24:27.162] [INFO ] Prepared 5328 feature-sample pairs
#> [2025-12-11 19:24:27.186] [INFO ] Exporting parameters to: data/interim/params/251211_192427_prepare_features_tables.yaml
#> [2025-12-11 19:24:27.200] [INFO ] Exported: example_features.tsv.gz (5,328 rows, 93.4 KB)
#> ✔ fea_pre completed [154ms, 95.63 kB]
#> + lib_sop_mer dispatched
#> [2025-12-11 19:24:27.589] [INFO ] Preparing merged structure-organism pairs library
#> [2025-12-11 19:24:34.638] [INFO ] Splitting SOP library into standardized components
#> [2025-12-11 19:24:35.936] [INFO ] Processing SMILES with RDKit
#> [2025-12-11 19:24:48.912] [INFO ] Processing 412 new SMILES with RDKit
#> 2025-12-11 19:24:48,915 - __main__ - INFO - Starting SMILES processing pipeline
#> 2025-12-11 19:24:48,915 - __main__ - INFO - Input: /tmp/RtmpraLwtt/file2126446cef1b.smi
#> 2025-12-11 19:24:48,915 - __main__ - INFO - Output: /tmp/RtmpraLwtt/file2126792d5c08.csv.gz
#> 2025-12-11 19:24:48,915 - __main__ - INFO - Input file validated: /tmp/RtmpraLwtt/file2126446cef1b.smi
#> 2025-12-11 19:24:48,915 - __main__ - INFO - Output file validated: /tmp/RtmpraLwtt/file2126792d5c08.csv.gz
#> 2025-12-11 19:24:48,915 - __main__ - INFO - Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> 2025-12-11 19:24:48,915 - __main__ - INFO - SMILES supplier initialized
#> [19:24:48] Explicit valence for atom # 1 N, 3, is greater than permitted
#> [19:24:48] ERROR: Could not sanitize molecule on line 352
#> [19:24:48] ERROR: Explicit valence for atom # 1 N, 3, is greater than permitted
#> [19:24:48] Explicit valence for atom # 0 P, 11, is greater than permitted
#> [19:24:48] ERROR: Could not sanitize molecule on line 353
#> [19:24:48] ERROR: Explicit valence for atom # 0 P, 11, is greater than permitted
#> [19:24:48] Explicit valence for atom # 21 N, 4, is greater than permitted
#> [19:24:48] ERROR: Could not sanitize molecule on line 354
#> [19:24:48] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
#> [19:24:48] Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [19:24:48] ERROR: Could not sanitize molecule on line 355
#> [19:24:48] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [19:24:48] Explicit valence for atom # 6 C, 5, is greater than permitted
#> [19:24:48] ERROR: Could not sanitize molecule on line 356
#> [19:24:48] ERROR: Explicit valence for atom # 6 C, 5, is greater than permitted
#> [19:24:48] Explicit valence for atom # 18 S, 7, is greater than permitted
#> [19:24:48] ERROR: Could not sanitize molecule on line 357
#> [19:24:48] ERROR: Explicit valence for atom # 18 S, 7, is greater than permitted
#> [19:24:48] 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
#> [19:24:48] SMILES Parse Error: check for mistakes around position 76:
#> [19:24:48] C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C
#> [19:24:48] ~~~~~~~~~~~~~~~~~~~~^
#> [19:24:48] 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
#> [19:24:48] SMILES Parse Error: check for mistakes around position 32:
#> [19:24:48] C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2
#> [19:24:48] ~~~~~~~~~~~~~~~~~~~~^
#> [19:24:48] 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
#> [19:24:48] SMILES Parse Error: check for mistakes around position 49:
#> [19:24:48] )\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2
#> [19:24:48] ~~~~~~~~~~~~~~~~~~~~^
#> [19:24:48] 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
#> [19:24:48] SMILES Parse Error: check for mistakes around position 66:
#> [19:24:48] )=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(
#> [19:24:48] ~~~~~~~~~~~~~~~~~~~~^
#> [19:24:48] 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'
#> [19:24:48] ERROR: Smiles parse error on line 358
#> [19:24:48] 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'
#> 2025-12-11 19:24:50,773 - __main__ - INFO - Processing complete. Total molecules processed: 405
#> [2025-12-11 19:24:50.811] [INFO ] Successfully processed 405 SMILES
#> [2025-12-11 19:25:11.306] [INFO ] Referenced structure-organism pairs (879,952)
#> [2025-12-11 19:25:15.718] [INFO ] Structures: 393,501 stereoisomers, 1,007,793 without stereochemistry, 1,184,324 constitutional isomers
#> [2025-12-11 19:25:35.344] [INFO ] Unique organisms (36,801)
#> [2025-12-11 19:25:35.428] [INFO ] Processing 919 organism name(s) for OTT taxonomy lookup
#> [2025-12-11 19:25:35.913] [INFO ] Querying OTT API in 10 batches
#> [2025-12-11 19:25:41.217] [INFO ] Retrieving detailed taxonomy for 13 unique OTT IDs
#> [2025-12-11 19:25:43.532] [INFO ] Got OTTaxonomy!
#> [2025-12-11 19:25:43.566] [INFO ] Exporting parameters to: data/interim/params/251211_192543_prepare_libraries_sop_merged.yaml
#> [2025-12-11 19:25:44.710] [INFO ] Exported: keys.tsv.gz (879,952 rows, 17.3 MB)
#> [2025-12-11 19:25:44.798] [INFO ] Exported: ott.tsv.gz (35,896 rows, 917.2 KB)
#> [2025-12-11 19:25:48.202] [INFO ] Exported: stereo.tsv.gz (1,404,576 rows, 41.6 MB)
#> [2025-12-11 19:25:49.866] [INFO ] Exported: metadata.tsv.gz (1,458,609 rows, 34.4 MB)
#> [2025-12-11 19:25:50.464] [INFO ] Exported: names.tsv.gz (423,335 rows, 10.8 MB)
#> [2025-12-11 19:25:50.614] [INFO ] Exported: classyfire.tsv.gz (146,393 rows, 2.4 MB)
#> [2025-12-11 19:25:50.908] [INFO ] Exported: npc.tsv.gz (141,818 rows, 2.3 MB)
#> ✔ lib_sop_mer completed [1m 23.3s, 114.86 MB]
#> + edg_spe dispatched
#> ✔ edg_spe completed [0ms, 437.86 kB]
#> + lib_mer_str_tax_npc dispatched
#> ✔ lib_mer_str_tax_npc completed [0ms, 2.44 MB]
#> + lib_mer_str_met dispatched
#> ✔ lib_mer_str_met completed [0ms, 36.03 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 [0ms, 43.58 MB]
#> + lib_mer_str_tax_cla dispatched
#> ✔ lib_mer_str_tax_cla completed [0ms, 2.51 MB]
#> + lib_mer_key dispatched
#> ✔ lib_mer_key completed [0ms, 18.09 MB]
#> + lib_mer_org_tax_ott dispatched
#> ✔ lib_mer_org_tax_ott completed [1ms, 939.19 kB]
#> + ann_sir_pre dispatched
#> [2025-12-11 19:25:54.979] [INFO ] Preparing SIRIUS v6 annotations
#> [2025-12-11 19:26:17.526] [INFO ] Exporting SIRIUS results to 3 files
#> [2025-12-11 19:26:17.548] [INFO ] Exporting parameters to: data/interim/params/251211_192617_prepare_annotations_sirius.yaml
#> [2025-12-11 19:26:17.550] [INFO ] Exported: example_canopusPrepared.tsv.gz (14 rows, 784 B)
#> [2025-12-11 19:26:17.552] [INFO ] Exported: example_formulaPrepared.tsv.gz (16 rows, 487 B)
#> [2025-12-11 19:26:17.557] [INFO ] Exported: example_siriusPrepared.tsv.gz (479 rows, 23.9 KB)
#> [2025-12-11 19:26:17.558] [INFO ] SIRIUS annotations prepared successfully
#> ✔ ann_sir_pre completed [22.6s, 25.71 kB]
#> + ann_spe_pre dispatched
#> [2025-12-11 19:26:18.382] [INFO ] Preparing spectral matching annotations from 2 file(s)
#> [2025-12-11 19:26:55.440] [INFO ] Exporting parameters to: data/interim/params/251211_192655_prepare_annotations_spectra.yaml
#> [2025-12-11 19:26:57.987] [INFO ] Exported: example_spectralMatchesPrepared.tsv.gz (568,675 rows, 51.1 MB)
#> ✔ ann_spe_pre completed [39.6s, 53.61 MB]
#> + ann_spe_exp_gnp_pre dispatched
#> [2025-12-11 19:26:58.906] [INFO ] Preparing GNPS annotations
#> [2025-12-11 19:26:58.908] [WARN ] No GNPS annotations found, returning an empty file instead
#> [2025-12-11 19:26:58.927] [INFO ] Exporting parameters to: data/interim/params/251211_192658_prepare_annotations_gnps.yaml
#> [2025-12-11 19:26:58.929] [INFO ] Exported: example_gnpsPrepared.tsv.gz (1 rows, 237 B)
#> ✔ ann_spe_exp_gnp_pre completed [28ms, 237 B]
#> + ann_ms1_pre dispatched
#> [2025-12-11 19:26:59.325] [INFO ] Starting mass-based annotation
#> [2025-12-11 19:26:59.361] [INFO ] Processing 5328 features for annotation
#> [2025-12-11 19:27:15.759] [INFO ] Already 2112 adducts previously detected
#> [2025-12-11 19:27:15.828] [INFO ] Here are the top 10 observed m/z differences inside the RT windows:
#> [2025-12-11 19:27:15.830] [INFO ] 
#>              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
#> [2025-12-11 19:27:15.831] [INFO ] These differences may help identify potential preprocessing issues
#> [2025-12-11 19:27:18.575] [WARN ] Failed to parse adduct '[M+2H]+2', cannot calculate neutral mass
#> [2025-12-11 19:27:18.888] [WARN ] Some adducts were unproperly detected, defaulting to (de)protonated
#> [2025-12-11 19:28:01.300] [INFO ] MS1 annotations: 48003 unique structures across 4237 features
#> [2025-12-11 19:28:01.351] [INFO ] Exporting parameters to: data/interim/params/251211_192801_annotate_masses.yaml
#> [2025-12-11 19:28:01.354] [INFO ] Exported: example_edgesMasses.tsv (2,653 rows, 79.8 KB)
#> [2025-12-11 19:28:02.094] [INFO ] Exported: example_ms1Prepared.tsv.gz (189,437 rows, 10.4 MB)
#> ✔ ann_ms1_pre completed [1m 2.8s, 10.97 MB]
#> + tax_pre dispatched
#> [2025-12-11 19:28:02.896] [INFO ] Preparing taxonomic assignments for features
#> [2025-12-11 19:28:02.897] [INFO ] Using metadata for organism assignments
#> [2025-12-11 19:28:03.047] [INFO ] Processing 2 organism name(s) for OTT taxonomy lookup
#> [2025-12-11 19:28:03.310] [INFO ] Querying OTT API in 1 batches
#> [2025-12-11 19:28:03.618] [INFO ] Retrying failed queries using genus names only
#> [2025-12-11 19:28:03.624] [INFO ] Retrying with 1 genus names: blk 
#> [2025-12-11 19:28:03.835] [INFO ] Retrieving detailed taxonomy for 1 unique OTT IDs
#> [2025-12-11 19:28:03.952] [INFO ] Got OTTaxonomy!
#> [2025-12-11 19:28:04.403] [INFO ] Exporting parameters to: data/interim/params/251211_192804_prepare_taxa.yaml
#> [2025-12-11 19:28:04.411] [INFO ] Exported: example_taxed.tsv.gz (5,328 rows, 19.2 KB)
#> ✔ tax_pre completed [1.5s, 19.70 kB]
#> + ann_sir_pre_can dispatched
#> ✔ ann_sir_pre_can completed [1ms, 784 B]
#> + ann_sir_pre_str dispatched
#> ✔ ann_sir_pre_str completed [0ms, 24.44 kB]
#> + ann_sir_pre_for dispatched
#> ✔ ann_sir_pre_for completed [0ms, 487 B]
#> + ann_ms1_pre_edg dispatched
#> ✔ ann_ms1_pre_edg completed [0ms, 81.71 kB]
#> + ann_ms1_pre_ann dispatched
#> ✔ ann_ms1_pre_ann completed [1ms, 10.89 MB]
#> + fea_edg_pre dispatched
#> [2025-12-11 19:28:06.516] [INFO ] Preparing molecular network edges
#> [2025-12-11 19:28:06.549] [INFO ] Prepared 14226 total edges
#> [2025-12-11 19:28:06.569] [INFO ] Exporting parameters to: data/interim/params/251211_192806_prepare_features_edges.yaml
#> [2025-12-11 19:28:06.573] [INFO ] Exported: example_edges.tsv (14,226 rows, 628.9 KB)
#> ✔ fea_edg_pre completed [59ms, 644.03 kB]
#> + ann_fil dispatched
#> [2025-12-11 19:28:06.909] [INFO ] Filtering annotations
#> [2025-12-11 19:28:06.947] [INFO ] Processing 5328 unique features for annotation filtering
#> [2025-12-11 19:28:11.347] [INFO ] Removing MS1 annotations superseded by spectral matches
#> [2025-12-11 19:28:14.034] [INFO ] Removed 72320 redundant MS1 annotations
#> [2025-12-11 19:28:14.036] [INFO ] Total annotations before RT filtering: 686272
#> [2025-12-11 19:28:15.268] [INFO ] Filtering annotations outside Inf min RT tolerance
#> [2025-12-11 19:28:18.787] [INFO ] Removed 0 annotations based on retention time tolerance
#> [2025-12-11 19:28:19.013] [INFO ] Exporting parameters to: data/interim/params/251211_192819_filter_annotations.yaml
#> [2025-12-11 19:28:21.744] [INFO ] Exported: example_annotationsFiltered.tsv.gz (686,859 rows, 49.5 MB)
#> ✔ ann_fil completed [14.8s, 51.87 MB]
#> + fea_com dispatched
#> [2025-12-11 19:28:22.431] [INFO ] Creating components from 1 edge file(s)
#> [2025-12-11 19:28:22.443] [INFO ] Loaded 12330 edges connecting 4572 unique features
#> [2025-12-11 19:28:22.451] [INFO ] Found 1493 components
#> [2025-12-11 19:28:22.461] [INFO ] Component sizes - Min: 1, Max: 2083, Mean: 3.1
#> [2025-12-11 19:28:22.476] [INFO ] Exporting parameters to: data/interim/params/251211_192822_create_components.yaml
#> [2025-12-11 19:28:22.478] [INFO ] Exported: example_components.tsv (4,572 rows, 38.1 KB)
#> [2025-12-11 19:28:22.479] [INFO ] Components written to: data/interim/features/example_components.tsv
#> ✔ fea_com completed [51ms, 39 kB]
#> + int_com dispatched
#> ✔ int_com completed [0ms, 39 kB]
#> + fea_com_pre dispatched
#> [2025-12-11 19:28:23.162] [INFO ] Prepared unique feature-component assignments (4,572)
#> [2025-12-11 19:28:23.178] [INFO ] Exporting parameters to: data/interim/params/251211_192823_prepare_features_components.yaml
#> [2025-12-11 19:28:23.181] [INFO ] Exported: example_componentsPrepared.tsv (4,572 rows, 38.1 KB)
#> ✔ fea_com_pre completed [24ms, 38.99 kB]
#> + ann_wei dispatched
#> [2025-12-11 19:28:23.509] [INFO ] Starting annotation weighting and scoring
#> [2025-12-11 19:28:41.155] [INFO ] 
#>  candidate_library      n
#>    ISDB - Wikidata 523258
#>           TIMA MS1  89384
#>               gnps  21785
#>             merlin  20309
#>           massbank   3222
#>             SIRIUS    479
#> [2025-12-11 19:28:48.633] [INFO ] Weighting 643352 annotations by biological source
#> [2025-12-11 19:28:53.878] [INFO ] Taxonomically informed metabolite annotation reranked:
#>     Kingdom level: 39531 structures
#>     Phylum level:  39085 structures
#>     Class level:   33489 structures
#>     Order level:   9169 structures
#>     Family level:  7380 structures
#>     Tribe level:   1245 structures
#>     Genus level:   985 structures
#>     Species level: 476 structures
#>     Variety level: 96 structures
#>     Biota level:   96 structures
#> [2025-12-11 19:29:08.850] [INFO ] Weighting 643339 annotations by chemical consistency
#> [2025-12-11 19:29:12.055] [INFO ] Chemically informed metabolite annotation reranked:
#>   Classyfire:
#>     Kingdom level:    28051 structures
#>     Superclass level: 27946 structures
#>     Class level:      25724 structures
#>     Parent level:     19928 structures
#>   NPClassifier:
#>     Pathway level:    28253 structures
#>     Superclass level: 27364 structures
#>     Class level:      20053 structures
#> [2025-12-11 19:29:12.065] [INFO ] Cleaning chemically weighted annotations
#> [2025-12-11 19:29:12.066] [INFO ] Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score
#> [2025-12-11 19:29:20.590] [INFO ] Sampling candidates for 3105 features with more than 7 candidates per score
#> [2025-12-11 19:29:20.684] [INFO ] [filtered]  Removed 15720 low-confidence candidates (92.7% of 16959 total)
#> [2025-12-11 19:29:20.685] [INFO ] [filtered]  1239 high-confidence candidates remaining (7.3%)
#> [2025-12-11 19:29:20.687] [INFO ] Summarizing annotation results
#> [2025-12-11 19:29:29.119] [INFO ] Summarizing annotation results
#> [2025-12-11 19:29:48.766] [INFO ] Annotation weighting complete in 85.3 s
#> [2025-12-11 19:29:48.788] [INFO ] Exporting parameters to: data/processed/20251211_192948_example/251211_192948_prepare_params.yaml
#> [2025-12-11 19:29:48.809] [INFO ] Exporting parameters to: data/processed/20251211_192948_example/251211_192948_prepare_params_advanced.yaml
#> [2025-12-11 19:29:48.814] [INFO ] Exported: example_results_mini.tsv (5,844 rows, 786.4 KB)
#> [2025-12-11 19:29:48.820] [INFO ] Exported: example_results_filtered.tsv (5,844 rows, 1.7 MB)
#> [2025-12-11 19:29:49.447] [INFO ] Exported: example_results.tsv (460,251 rows, 269.7 MB)
#> [2025-12-11 19:29:49.449] [INFO ] Results exported: example_results.tsv
#> ✔ ann_wei completed [1m 25.9s, 284.52 MB]
#> ✔ ended pipeline [18m 36.7s, 130 completed, 0 skipped]
#> There were 15 warnings (use warnings() to see them)

The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!

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Citation

BibTeX citation:
@online{rutz2025,
  author = {Rutz, Adriano},
  title = {3 {Performing} {Taxonomically} {Informed} {Metabolite}
    {Annotation}},
  date = {2025-12-11},
  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.” December 11, 2025. https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/III-processing.html.