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 [1ms, 1.42 kB]
#> + par_def_pre_lib_sop_lot dispatched
#> ✔ par_def_pre_lib_sop_lot completed [0ms, 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 [0ms, 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 [0ms, 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 [0ms, 706 B]
#> + par_def_pre_fea_tab dispatched
#> ✔ par_def_pre_fea_tab completed [1ms, 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 [2ms, 2.55 kB]
#> + lib_spe_exp_mer_pre_pos dispatched
#> [2025-12-28 23:01:43.464] [INFO ] > Starting: download_file [url=https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/merlin_13911806_pos.rds, destination=data/interim/libraries/spectra/exp/merlin_13911806_pos.rds]
#> [2025-12-28 23:01:43.886] [INFO ] [OK] Completed: download_file [size_bytes=84936306] (395ms)
#> ✔ lib_spe_exp_mer_pre_pos completed [453ms, 84.94 MB]
#> + lib_spe_exp_mer_pre_neg dispatched
#> [2025-12-28 23:01:44.079] [INFO ] > Starting: download_file [url=https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/merlin_13911806_neg.rds, destination=data/interim/libraries/spectra/exp/merlin_13911806_neg.rds]
#> [2025-12-28 23:01:44.274] [INFO ] [OK] Completed: download_file [size_bytes=31540426] (196ms)
#> ✔ lib_spe_exp_mer_pre_neg completed [197ms, 31.54 MB]
#> + lib_spe_exp_gnp_pre_pos dispatched
#> [2025-12-28 23:01:44.440] [INFO ] > Starting: download_file [url=https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/gnps_11566051_pos.rds, destination=data/interim/libraries/spectra/exp/gnps_11566051_pos.rds]
#> [2025-12-28 23:01:45.798] [INFO ] [OK] Completed: download_file [size_bytes=481271483] (1.4s)
#> ✔ lib_spe_exp_gnp_pre_pos completed [1.4s, 481.27 MB]
#> + lib_spe_exp_mb_pre_pos dispatched
#> [2025-12-28 23:01:46.127] [INFO ] > Starting: download_file [url=https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/massbank_2025051_pos.rds, destination=data/interim/libraries/spectra/exp/massbank_2025051_pos.rds]
#> [2025-12-28 23:01:46.408] [INFO ] [OK] Completed: download_file [size_bytes=19411864] (281ms)
#> ✔ lib_spe_exp_mb_pre_pos completed [283ms, 19.41 MB]
#> + lib_spe_is_wik_pre_pos dispatched
#> [2025-12-28 23:01:46.573] [INFO ] > Starting: download_file [url=https://github.com/taxonomicallyinformedannotation/tima-isdb-pos/raw/main/wikidata_5607185_pos.rds, destination=data/interim/libraries/spectra/is/wikidata_5607185_pos.rds]
#> Downloading 44% ■■■■■■■■■■■■■■ 1s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 0s
#> [2025-12-28 23:01:48.978] [INFO ] [OK] Completed: download_file [size_bytes=863950396] (2.4s)
#> ✔ lib_spe_is_wik_pre_pos completed [2.4s, 863.95 MB]
#> + par_pre_par dispatched
#> ✔ par_pre_par completed [0ms, 1.38 kB]
#> + par_pre_par2 dispatched
#> ✔ par_pre_par2 completed [1ms, 21.68 kB]
#> + lib_sop_hmd dispatched
#> [2025-12-28 23:01:49.743] [INFO ] > Starting: download_file [url=https://hmdb.ca/system/downloads/current/structures.zip, destination=data/source/libraries/sop/hmdb/structures.zip]
#> Downloading 0% ■ 21m
#> Downloading 0% ■ 21m
#> Downloading 0% ■ 22m
#> Downloading 1% ■ 23m
#> Downloading 1% ■ 15m
#> Downloading 2% ■■ 14m
#> Downloading 2% ■■ 15m
#> Downloading 2% ■■ 16m
#> Downloading 2% ■■ 17m
#> Downloading 2% ■■ 18m
#> Downloading 3% ■■ 19m
#> Downloading 3% ■■ 20m
#> Downloading 3% ■■ 21m
#> Downloading 3% ■■ 22m
#> Downloading 3% ■■ 23m
#> Downloading 3% ■■ 24m
#> Downloading 3% ■■ 24m
#> Downloading 3% ■■ 24m
#> Downloading 4% ■■ 24m
#> Downloading 4% ■■ 24m
#> Downloading 4% ■■ 25m
#> Downloading 4% ■■ 26m
#> Downloading 4% ■■ 27m
#> Downloading 4% ■■ 27m
#> Downloading 5% ■■ 25m
#> Downloading 5% ■■ 26m
#> Downloading 5% ■■ 25m
#> Downloading 5% ■■■ 26m
#> Downloading 5% ■■■ 26m
#> Downloading 5% ■■■ 27m
#> [2025-12-28 23:03:19.032] [WARN ] file download failed (attempt 1/3), retrying in 1s: Failed to perform HTTP request.
#> Caused by error in `curl::curl_fetch_disk()`:
#> ! Transferred a partial file [hmdb.ca]:
#> transfer closed with 91425375 bytes remaining to read
#> Downloading 5% ■■■ 27m
#> Downloading 39% ■■■■■■■■■■■■■ 2s
#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 0s
#> [2025-12-28 23:03:23.193] [INFO ] [OK] Completed: download_file [size_bytes=96479839] (1m 33s)
#> ✔ lib_sop_hmd completed [1m 33.5s, 96.48 MB]
#> + lib_sop_ecm dispatched
#> [2025-12-28 23:03:23.387] [INFO ] > Starting: download_file [url=https://ecmdb.ca/download/ecmdb.json.zip, destination=data/source/libraries/sop/ecmdb.json.zip]
#> [2025-12-28 23:03:24.466] [INFO ] [OK] Completed: download_file [size_bytes=1334921] (1.1s)
#> ✔ lib_sop_ecm completed [1.1s, 1.33 MB]
#> + lib_spe_exp_mer_pre_sop dispatched
#> [2025-12-28 23:03:24.623] [INFO ] > Starting: download_file [url=https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/merlin_13911806_prepared.tsv.gz, destination=data/interim/libraries/sop/merlin_13911806_prepared.tsv.gz]
#> [2025-12-28 23:03:24.824] [INFO ] [OK] Completed: download_file [size_bytes=1190284] (201ms)
#> ✔ lib_spe_exp_mer_pre_sop completed [202ms, 1.19 MB]
#> + lib_sop_lot dispatched
#> [2025-12-28 23:03:24.979] [INFO ] Retrieving latest version from Zenodo: 10.5281/zenodo.5794106
#> [2025-12-28 23:03:26.793] [INFO ] Downloading 230106_frozen_metadata.csv.gz from https://doi.org/10.5281/zenodo.5794106
#> [2025-12-28 23:03:26.795] [INFO ] > Starting: download_file [url=https://zenodo.org/records/7534071/files/230106_frozen_metadata.csv.gz, destination=data/source/libraries/sop/lotus.csv.gz]
#> [2025-12-28 23:04:26.684] [INFO ] [OK] Completed: download_file [size_bytes=92979778] (59.9s)
#> [2025-12-28 23:04:26.686] [INFO ] Download completed: data/source/libraries/sop/lotus.csv.gz
#> ✔ lib_sop_lot completed [1m 1.7s, 92.98 MB]
#> + lib_spe_is_wik_pre_neg dispatched
#> [2025-12-28 23:04:26.878] [INFO ] > Starting: download_file [url=https://github.com/taxonomicallyinformedannotation/tima-isdb-neg/raw/main/wikidata_5607185_neg.rds, destination=data/interim/libraries/spectra/is/wikidata_5607185_neg.rds]
#> [2025-12-28 23:04:28.868] [INFO ] [OK] Completed: download_file [size_bytes=687328159] (2s)
#> ✔ lib_spe_is_wik_pre_neg completed [2s, 687.33 MB]
#> + lib_spe_exp_mb_pre_sop dispatched
#> [2025-12-28 23:04:29.266] [INFO ] > Starting: download_file [url=https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/massbank_2025051_prepared.tsv.gz, destination=data/interim/libraries/sop/massbank_2025051_prepared.tsv.gz]
#> [2025-12-28 23:04:29.373] [INFO ] [OK] Completed: download_file [size_bytes=480970] (107ms)
#> ✔ lib_spe_exp_mb_pre_sop completed [108ms, 480.97 kB]
#> + lib_spe_exp_gnp_pre_sop dispatched
#> [2025-12-28 23:04:29.538] [INFO ] > Starting: download_file [url=https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz, destination=data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz]
#> [2025-12-28 23:04:29.706] [INFO ] [OK] Completed: download_file [size_bytes=1416699] (168ms)
#> ✔ lib_spe_exp_gnp_pre_sop completed [169ms, 1.42 MB]
#> + lib_spe_is_wik_pre_sop dispatched
#> [2025-12-28 23:04:29.860] [INFO ] > Starting: download_file [url=https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/wikidata_spectral_5607185_prepared.tsv.gz, destination=data/interim/libraries/sop/wikidata_5607185_prepared.tsv.gz]
#> [2025-12-28 23:04:30.045] [INFO ] [OK] Completed: download_file [size_bytes=37904410] (184ms)
#> ✔ lib_spe_is_wik_pre_sop completed [186ms, 37.90 MB]
#> + lib_spe_exp_gnp_pre_neg dispatched
#> [2025-12-28 23:04:30.217] [INFO ] > Starting: download_file [url=https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/gnps_11566051_neg.rds, destination=data/interim/libraries/spectra/exp/gnps_11566051_neg.rds]
#> [2025-12-28 23:04:30.709] [INFO ] [OK] Completed: download_file [size_bytes=154124724] (492ms)
#> ✔ lib_spe_exp_gnp_pre_neg completed [493ms, 154.12 MB]
#> + lib_spe_exp_mb_pre_neg dispatched
#> [2025-12-28 23:04:30.921] [INFO ] > Starting: download_file [url=https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/massbank_2025051_neg.rds, destination=data/interim/libraries/spectra/exp/massbank_2025051_neg.rds]
#> [2025-12-28 23:04:31.008] [INFO ] [OK] Completed: download_file [size_bytes=7057574] (87ms)
#> ✔ lib_spe_exp_mb_pre_neg completed [89ms, 7.06 MB]
#> + par_fin_par dispatched
#> ✔ par_fin_par completed [1ms, 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 [1.5s, 731 B]
#> + par_usr_ann_spe dispatched
#> ✔ par_usr_ann_spe completed [1.4s, 1.01 kB]
#> + par_usr_wei_ann dispatched
#> ✔ par_usr_wei_ann completed [1.4s, 1.80 kB]
#> + par_usr_pre_lib_sop_ecm dispatched
#> ✔ par_usr_pre_lib_sop_ecm completed [1.4s, 176 B]
#> + par_usr_ann_mas dispatched
#> ✔ par_usr_ann_mas completed [1.4s, 2.68 kB]
#> + par_usr_pre_fea_edg dispatched
#> ✔ par_usr_pre_fea_edg completed [1.4s, 328 B]
#> + par_usr_fil_ann dispatched
#> ✔ par_usr_fil_ann completed [1.4s, 668 B]
#> + par_usr_pre_lib_sop_lot dispatched
#> ✔ par_usr_pre_lib_sop_lot completed [1.4s, 174 B]
#> + par_usr_pre_ann_sir dispatched
#> ✔ par_usr_pre_ann_sir completed [1.5s, 900 B]
#> + par_usr_pre_lib_spe dispatched
#> ✔ par_usr_pre_lib_spe completed [1.4s, 298 B]
#> + par_usr_pre_lib_sop_mer dispatched
#> ✔ par_usr_pre_lib_sop_mer completed [1.4s, 1.60 kB]
#> + par_usr_pre_fea_com dispatched
#> ✔ par_usr_pre_fea_com completed [1.4s, 200 B]
#> + par_usr_pre_lib_sop_big dispatched
#> ✔ par_usr_pre_lib_sop_big completed [1.4s, 107 B]
#> + par_usr_pre_ann_gnp dispatched
#> ✔ par_usr_pre_ann_gnp completed [1.4s, 708 B]
#> + par_usr_cre_com dispatched
#> ✔ par_usr_cre_com completed [1.4s, 200 B]
#> + par_usr_pre_lib_sop_hmd dispatched
#> ✔ par_usr_pre_lib_sop_hmd completed [1.4s, 178 B]
#> + par_usr_cre_edg_spe dispatched
#> ✔ par_usr_cre_edg_spe completed [1.4s, 434 B]
#> + par_usr_pre_fea_tab dispatched
#> ✔ par_usr_pre_fea_tab completed [1.4s, 274 B]
#> + par_usr_pre_lib_rt dispatched
#> ✔ par_usr_pre_lib_rt completed [1.4s, 487 B]
#> + par_usr_pre_lib_sop_clo dispatched
#> ✔ par_usr_pre_lib_sop_clo completed [1.4s, 267 B]
#> + par_usr_pre_tax dispatched
#> ✔ par_usr_pre_tax completed [1.4s, 438 B]
#> + par_pre_ann_spe dispatched
#> ✔ par_pre_ann_spe completed [2ms, 334 B]
#> + par_ann_spe dispatched
#> ✔ par_ann_spe completed [1ms, 495 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 [3ms, 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 [1ms, 186 B]
#> + par_pre_ann_sir dispatched
#> ✔ par_pre_ann_sir completed [1ms, 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 [1ms, 387 B]
#> + par_pre_fea_tab dispatched
#> ✔ par_pre_fea_tab completed [1ms, 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
#> [2025-12-28 23:05:08.086] [INFO ] Preparing ECMDB structure-organism pairs
#> [2025-12-28 23:05:08.756] [INFO ] Exporting parameters to: data/interim/params/251228_230508_prepare_libraries_sop_ecmdb.yaml
#> [2025-12-28 23:05:08.759] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/ecmdb_prepared.tsv.gz, n_rows=3760]
#> [2025-12-28 23:05:08.774] [INFO ] [OK] Completed: export_output [size_bytes=177466] (16ms)
#> ✔ lib_sop_ecm_pre completed [689ms, 177.47 kB]
#> + lib_sop_lot_pre dispatched
#> [2025-12-28 23:05:08.950] [INFO ] > Starting: prepare_libraries_sop_lotus [input=data/source/libraries/sop/lotus.csv.gz]
#> [2025-12-28 23:05:19.410] [INFO ] [OK] Completed: prepare_libraries_sop_lotus [n_pairs=791809] (10.5s)
#> [2025-12-28 23:05:19.411] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/lotus_prepared.tsv.gz, n_rows=791809]
#> [2025-12-28 23:05:22.875] [INFO ] [OK] Completed: export_output [size_bytes=46518841] (3.5s)
#> ✔ lib_sop_lot_pre completed [13.9s, 46.52 MB]
#> + lib_spe_exp_int_pre dispatched
#> [2025-12-28 23:05:23.231] [INFO ] Preparing spectral library: internal
#> [2025-12-28 23:05:23.236] [WARN ] Input file(s) not found; creating empty library template
#> [2025-12-28 23:05:24.521] [INFO ] Exporting spectral library files
#> [2025-12-28 23:05:24.525] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/internal_prepared.tsv.gz, n_rows=1]
#> [2025-12-28 23:05:24.527] [INFO ] [OK] Completed: export_output [size_bytes=106] (1ms)
#> [2025-12-28 23:05:24.591] [INFO ] Exporting parameters to: data/interim/params/251228_230524_prepare_libraries_spectra.yaml
#> [2025-12-28 23:05:24.592] [INFO ] Spectral library 'internal' prepared successfully
#> ✔ lib_spe_exp_int_pre completed [1.4s, 1.30 kB]
#> + lib_sop_mer_str_pro dispatched
#> [2025-12-28 23:05:24.946] [INFO ] > Starting: download_file [url=https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/processed.csv.gz, destination=data/interim/libraries/sop/merged/structures/processed.csv.gz]
#> [2025-12-28 23:05:25.300] [INFO ] [OK] Completed: download_file [size_bytes=80668186] (354ms)
#> ✔ lib_sop_mer_str_pro completed [358ms, 80.67 MB]
#> + lib_sop_big_pre dispatched
#> [2025-12-28 23:05:25.614] [INFO ] Preparing BiGG structure-organism pairs
#> [2025-12-28 23:05:49.090] [INFO ] > Starting: process_smiles [n_structures=1417]
#> [2025-12-28 23:05:49.091] [INFO ] Processing SMILES with RDKit
#> [2025-12-28 23:05:49.961] [INFO ] Processing 1416 new SMILES with RDKit
#> [2025-12-28 23:05:49.963] [INFO ] Starting SMILES processing pipeline
#> [2025-12-28 23:05:49.963] [INFO ] Input: /tmp/Rtmp9oDSfr/file217639978d17.smi
#> [2025-12-28 23:05:49.963] [INFO ] Output: /tmp/Rtmp9oDSfr/file21763c16bb68.csv.gz
#> [2025-12-28 23:05:49.964] [INFO ] Input file validated: /tmp/Rtmp9oDSfr/file217639978d17.smi
#> [2025-12-28 23:05:49.964] [INFO ] Output file validated: /tmp/Rtmp9oDSfr/file21763c16bb68.csv.gz
#> [2025-12-28 23:05:49.964] [INFO ] Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> [2025-12-28 23:05:49.964] [INFO ] SMILES supplier initialized
#> [2025-12-28 23:05:51.963] [INFO ] Processing complete. Total molecules processed: 1416
#> [2025-12-28 23:05:51.999] [INFO ] Successfully processed 1416 SMILES
#> [2025-12-28 23:05:52.008] [INFO ] [OK] Completed: process_smiles [n_processed=1416] (2.9s)
#> [2025-12-28 23:06:00.000] [INFO ] > Starting: process_smiles [n_structures=2083]
#> [2025-12-28 23:06:00.001] [INFO ] Processing SMILES with RDKit
#> [2025-12-28 23:06:00.012] [INFO ] Processing 1240 new SMILES with RDKit
#> [2025-12-28 23:06:00.014] [INFO ] Starting SMILES processing pipeline
#> [2025-12-28 23:06:00.014] [INFO ] Input: /tmp/Rtmp9oDSfr/file217623b1d8b5.smi
#> [2025-12-28 23:06:00.014] [INFO ] Output: /tmp/Rtmp9oDSfr/file21765c3b1b3.csv.gz
#> [2025-12-28 23:06:00.014] [INFO ] Input file validated: /tmp/Rtmp9oDSfr/file217623b1d8b5.smi
#> [2025-12-28 23:06:00.014] [INFO ] Output file validated: /tmp/Rtmp9oDSfr/file21765c3b1b3.csv.gz
#> [2025-12-28 23:06:00.014] [INFO ] Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> [2025-12-28 23:06:00.014] [INFO ] SMILES supplier initialized
#> [2025-12-28 23:06:01.803] [INFO ] Processing complete. Total molecules processed: 1240
#> [2025-12-28 23:06:01.839] [INFO ] Successfully processed 1240 SMILES
#> [2025-12-28 23:06:01.846] [INFO ] [OK] Completed: process_smiles [n_processed=1240] (1.8s)
#> [2025-12-28 23:06:01.924] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/bigg_prepared.tsv.gz, n_rows=2353]
#> [2025-12-28 23:06:01.937] [INFO ] [OK] Completed: export_output [size_bytes=85310] (13ms)
#> ✔ lib_sop_big_pre completed [36.3s, 85.31 kB]
#> + lib_sop_hmd_pre dispatched
#> [2025-12-28 23:06:02.299] [INFO ] > Starting: prepare_libraries_sop_hmdb [input=data/source/libraries/sop/hmdb/structures.zip]
#> [2025-12-28 23:06:46.751] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/hmdb_prepared.tsv.gz, n_rows=217776]
#> [2025-12-28 23:06:47.362] [INFO ] [OK] Completed: export_output [size_bytes=8058153] (610ms)
#> [2025-12-28 23:06:47.363] [INFO ] [OK] Completed: prepare_libraries_sop_hmdb [n_pairs=217776] (45.1s)
#> ✔ lib_sop_hmd_pre completed [45.1s, 8.06 MB]
#> + par_pre_fea_tab_fil_fea_raw dispatched
#> ✔ par_pre_fea_tab_fil_fea_raw completed [0ms, 451.55 kB]
#> + lib_rt dispatched
#> [2025-12-28 23:06:48.406] [INFO ] Preparing retention time libraries
#> [2025-12-28 23:06:48.418] [WARN ] No retention time library found, returning empty retention time and sop tables.
#> [2025-12-28 23:06:48.462] [INFO ] Exporting parameters to: data/interim/params/251228_230648_prepare_libraries_rt.yaml
#> [2025-12-28 23:06:48.463] [INFO ] > Starting: export_output [file=data/interim/libraries/rt/prepared.tsv.gz, n_rows=1]
#> [2025-12-28 23:06:48.465] [INFO ] [OK] Completed: export_output [size_bytes=86] (1ms)
#> [2025-12-28 23:06:48.467] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/rt_prepared.tsv.gz, n_rows=1]
#> [2025-12-28 23:06:48.469] [INFO ] [OK] Completed: export_output [size_bytes=105] (1ms)
#> ✔ lib_rt completed [66ms, 191 B]
#> + lib_sop_clo_pre dispatched
#> [2025-12-28 23:06:48.806] [INFO ] Preparing closed structure-organism pairs library
#> [2025-12-28 23:06:48.807] [WARN ] Closed resource not accessible at: ~/Git/lotus-processor/data/processed/240412_closed_metadata.csv.gz. Returning empty template instead.
#> [2025-12-28 23:06:48.823] [INFO ] Exporting parameters to: data/interim/params/251228_230648_prepare_libraries_sop_closed.yaml
#> [2025-12-28 23:06:48.825] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/closed_prepared.tsv.gz, n_rows=1]
#> [2025-12-28 23:06:48.826] [INFO ] [OK] Completed: export_output [size_bytes=273] (1ms)
#> ✔ lib_sop_clo_pre completed [22ms, 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
#> [2025-12-28 23:06:51.567] [INFO ] > Starting: create_edges_spectra [method=gnps, threshold=0.7, n_input_files=1]
#> [2025-12-28 23:06:51.568] [INFO ] Creating spectral similarity network edges
#> [2025-12-28 23:06:51.569] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-12-28 23:06:51.597] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-12-28 23:06:53.264] [INFO ] Processed 10000 spectra...
#> [2025-12-28 23:06:54.466] [INFO ] Total spectra read: 16282
#> [2025-12-28 23:07:00.162] [INFO ] Loaded 16282 spectra from file
#> [2025-12-28 23:07:00.175] [INFO ] Combining replicate spectra by FEATURE_ID
#> [2025-12-28 23:07:02.533] [INFO ] Combined replicates: 12195 -> 4087 spectra
#> [2025-12-28 23:07:02.535] [INFO ] Sanitizing 4087 spectra (cutoff: dynamic)
#> [2025-12-28 23:07:03.741] [INFO ] Sanitization complete: 3281/4087 spectra retained (80.3%, 806 removed)
#> [2025-12-28 23:07:03.742] [INFO ] Import complete: 3281 spectra ready for analysis
#> [2025-12-28 23:07:03.743] [INFO ] ======================================
#> [2025-12-28 23:07:03.743] [INFO ] Take yourself a break, you deserve it.
#> [2025-12-28 23:07:03.744] [INFO ] ======================================
#> [2025-12-28 23:08:09.262] [INFO ] Processed 500 / 3280 queries
#> [2025-12-28 23:09:05.583] [INFO ] Processed 1000 / 3280 queries
#> [2025-12-28 23:09:49.274] [INFO ] Processed 1500 / 3280 queries
#> [2025-12-28 23:10:22.473] [INFO ] Processed 2000 / 3280 queries
#> [2025-12-28 23:10:45.332] [INFO ] Processed 2500 / 3280 queries
#> [2025-12-28 23:10:56.979] [INFO ] Processed 3000 / 3280 queries
#> [2025-12-28 23:10:58.804] [INFO ] Here is the distribution of edge similarity scores (0.1 bins) BEFORE filtering:
#> [2025-12-28 23:10:58.806] [INFO ]
#> bin N
#> [0,0.1] 3973900
#> (0.1,0.2] 855247
#> (0.2,0.3] 306315
#> (0.3,0.4] 127474
#> (0.4,0.5] 58050
#> (0.5,0.6] 29498
#> (0.6,0.7] 15742
#> (0.7,0.8] 8198
#> (0.8,0.9] 4629
#> (0.9,1] 1787
#> [2025-12-28 23:10:58.811] [INFO ] Created 7199 edges passing thresholds
#> [2025-12-28 23:10:58.883] [INFO ] Exporting parameters to: data/interim/params/251228_231058_create_edges_spectra.yaml
#> [2025-12-28 23:10:58.885] [INFO ] > Starting: export_output [file=data/interim/features/example_edgesSpectra.tsv, n_rows=9138]
#> [2025-12-28 23:10:58.889] [INFO ] [OK] Completed: export_output [size_bytes=433428] (3ms)
#> [2025-12-28 23:10:58.890] [INFO ] [OK] Completed: create_edges_spectra [n_edges=9138] (4m 7s)
#> ✔ fea_edg_spe completed [4m 7.3s, 433.43 kB]
#> + ann_spe_pos dispatched
#> [2025-12-28 23:10:59.339] [INFO ] ============================================================
#> [2025-12-28 23:10:59.340] [INFO ] Data Sanitizing: Pre-flight Checks
#> [2025-12-28 23:10:59.340] [INFO ] ============================================================
#> [2025-12-28 23:10:59.341] [INFO ] Checking MGF file...
#> [2025-12-28 23:11:00.377] [INFO ] [OK] MGF file: 12195 MS2 spectra found
#> [2025-12-28 23:11:00.378] [INFO ] ============================================================
#> [2025-12-28 23:11:00.379] [INFO ] [OK] All pre-flight checks passed!
#> [2025-12-28 23:11:00.380] [INFO ] Data validation complete. Ready to proceed.
#> [2025-12-28 23:11:00.381] [INFO ] ============================================================
#> [2025-12-28 23:11:00.382] [INFO ] Starting spectral annotation in pos mode
#> [2025-12-28 23:11:00.383] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-12-28 23:11:00.384] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-12-28 23:11:02.117] [INFO ] Processed 10000 spectra...
#> [2025-12-28 23:11:03.252] [INFO ] Total spectra read: 16282
#> [2025-12-28 23:11:08.771] [INFO ] Loaded 16282 spectra from file
#> [2025-12-28 23:11:08.784] [INFO ] Combining replicate spectra by FEATURE_ID
#> [2025-12-28 23:11:09.558] [INFO ] Combined replicates: 12195 -> 4087 spectra
#> [2025-12-28 23:11:09.560] [INFO ] Sanitizing 4087 spectra (cutoff: dynamic)
#> [2025-12-28 23:11:10.857] [INFO ] Sanitization complete: 3281/4087 spectra retained (80.3%, 806 removed)
#> [2025-12-28 23:11:10.858] [INFO ] Import complete: 3281 spectra ready for analysis
#> [2025-12-28 23:11:10.860] [INFO ] Importing spectra from: data/interim/libraries/spectra/is/wikidata_5607185_pos.rds
#> [2025-12-28 23:11:33.236] [INFO ] Loaded 998198 spectra from file
#> [2025-12-28 23:11:33.861] [INFO ] Import complete: 998198 spectra ready for analysis
#> [2025-12-28 23:11:33.862] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/internal_pos.rds
#> [2025-12-28 23:11:33.863] [INFO ] Loaded 1 spectra from file
#> [2025-12-28 23:11:33.865] [INFO ] Import complete: 0 spectra ready for analysis
#> [2025-12-28 23:11:33.866] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/gnps_11566051_pos.rds
#> [2025-12-28 23:11:41.519] [INFO ] Loaded 354789 spectra from file
#> [2025-12-28 23:11:41.727] [INFO ] Import complete: 354788 spectra ready for analysis
#> [2025-12-28 23:11:41.729] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/massbank_2025051_pos.rds
#> [2025-12-28 23:11:42.456] [INFO ] Loaded 66388 spectra from file
#> [2025-12-28 23:11:42.512] [INFO ] Import complete: 66388 spectra ready for analysis
#> [2025-12-28 23:11:42.514] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/merlin_13911806_pos.rds
#> [2025-12-28 23:11:47.238] [INFO ] Loaded 208280 spectra from file
#> [2025-12-28 23:11:47.397] [INFO ] Import complete: 208273 spectra ready for analysis
#> [2025-12-28 23:12:00.190] [INFO ]
#> library spectra unique_connectivities
#> ISDB - Wikidata 998198 998198
#> gnps 354788 22675
#> merlin 208273 26197
#> massbank 66388 5901
#> [2025-12-28 23:12:01.402] [INFO ] > Starting: calculate_entropy_similarity [n_library=478616, n_query=3281, method=gnps]
#> [2025-12-28 23:12:01.403] [INFO ] Calculating entropy and similarity for 3281 spectra
#> [2025-12-28 23:12:47.983] [INFO ] Processed 500 / 3281 queries
#> [2025-12-28 23:13:30.147] [INFO ] Processed 1000 / 3281 queries
#> [2025-12-28 23:14:10.378] [INFO ] Processed 1500 / 3281 queries
#> [2025-12-28 23:14:46.920] [INFO ] Processed 2000 / 3281 queries
#> [2025-12-28 23:15:22.963] [INFO ] Processed 2500 / 3281 queries
#> [2025-12-28 23:16:01.625] [INFO ] Processed 3000 / 3281 queries
#> [2025-12-28 23:16:23.118] [INFO ] [OK] Completed: calculate_entropy_similarity [n_comparisons=910214] (4m 22s)
#> [2025-12-28 23:16:23.130] [INFO ] > Starting: harmonize_adducts [n_rows=478616]
#> [2025-12-28 23:16:24.815] [INFO ] [OK] Completed: harmonize_adducts [n_unique_before=48, n_unique_after=48] (1.7s)
#> [2025-12-28 23:16:25.951] [INFO ] Here is the distribution of annotation similarity scores (0.1 bins):
#> [2025-12-28 23:16:25.952] [INFO ]
#> bin N
#> [0,0.1] 467250
#> (0.1,0.2] 57422
#> (0.2,0.3] 21963
#> (0.3,0.4] 9847
#> (0.4,0.5] 4495
#> (0.5,0.6] 1957
#> (0.6,0.7] 682
#> (0.7,0.8] 460
#> (0.8,0.9] 363
#> (0.9,1] 170
#> [2025-12-28 23:16:26.005] [INFO ] 296732 Candidates annotated on 3126 features (threshold >= 0).
#> [2025-12-28 23:16:26.007] [INFO ] Exporting parameters to: data/interim/params/251228_231626_annotate_spectra.yaml
#> [2025-12-28 23:16:26.009] [INFO ] > Starting: export_output [file=data/interim/annotations/example_spectralMatches_pos.tsv.gz, n_rows=564609]
#> [2025-12-28 23:16:27.561] [INFO ] [OK] Completed: export_output [size_bytes=32950149] (1.6s)
#> ✔ ann_spe_pos completed [5m 28.3s, 32.95 MB]
#> + ann_spe_neg dispatched
#> [2025-12-28 23:16:29.140] [INFO ] ============================================================
#> [2025-12-28 23:16:29.141] [INFO ] Data Sanitizing: Pre-flight Checks
#> [2025-12-28 23:16:29.142] [INFO ] ============================================================
#> [2025-12-28 23:16:29.143] [INFO ] Checking MGF file...
#> [2025-12-28 23:16:30.251] [INFO ] [OK] MGF file: 12195 MS2 spectra found
#> [2025-12-28 23:16:30.252] [INFO ] ============================================================
#> [2025-12-28 23:16:30.254] [INFO ] [OK] All pre-flight checks passed!
#> [2025-12-28 23:16:30.255] [INFO ] Data validation complete. Ready to proceed.
#> [2025-12-28 23:16:30.256] [INFO ] ============================================================
#> [2025-12-28 23:16:30.257] [INFO ] Starting spectral annotation in neg mode
#> [2025-12-28 23:16:30.258] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-12-28 23:16:30.259] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-12-28 23:16:32.033] [INFO ] Processed 10000 spectra...
#> [2025-12-28 23:16:33.141] [INFO ] Total spectra read: 16282
#> [2025-12-28 23:16:38.452] [INFO ] Loaded 16282 spectra from file
#> [2025-12-28 23:16:38.462] [INFO ] Combining replicate spectra by FEATURE_ID
#> [2025-12-28 23:16:38.467] [INFO ] Combined replicates: 0 -> 0 spectra
#> [2025-12-28 23:16:38.468] [WARN ] No spectra to sanitize
#> [2025-12-28 23:16:38.469] [INFO ] Import complete: 0 spectra ready for analysis
#> [2025-12-28 23:16:38.470] [WARN ] No query spectra loaded
#> [2025-12-28 23:16:38.473] [INFO ] Exporting parameters to: data/interim/params/251228_231638_annotate_spectra.yaml
#> [2025-12-28 23:16:38.475] [WARN ] Returning empty annotation template
#> [2025-12-28 23:16:38.477] [INFO ] > Starting: export_output [file=data/interim/annotations/example_spectralMatches_neg.tsv.gz, n_rows=1]
#> [2025-12-28 23:16:38.479] [INFO ] [OK] Completed: export_output [size_bytes=237] (2ms)
#> ✔ ann_spe_neg completed [9.5s, 237 B]
#> + fea_pre dispatched
#> [2025-12-28 23:16:39.200] [INFO ] > Starting: prepare_features_tables [input=data/source/example_features.csv, candidates=1]
#> [2025-12-28 23:16:39.312] [INFO ] Prepared 5328 feature-sample pairs
#> [2025-12-28 23:16:39.314] [INFO ] [OK] Completed: prepare_features_tables [n_features=5328] (114ms)
#> [2025-12-28 23:16:39.338] [INFO ] Exporting parameters to: data/interim/params/251228_231639_prepare_features_tables.yaml
#> [2025-12-28 23:16:39.340] [INFO ] > Starting: export_output [file=data/interim/features/example_features.tsv.gz, n_rows=5328]
#> [2025-12-28 23:16:39.354] [INFO ] [OK] Completed: export_output [size_bytes=95629] (14ms)
#> ✔ fea_pre completed [158ms, 95.63 kB]
#> + lib_sop_mer dispatched
#> [2025-12-28 23:16:39.721] [INFO ] Preparing merged structure-organism pairs library
#> [2025-12-28 23:16:46.546] [INFO ] Splitting SOP library into standardized components
#> [2025-12-28 23:16:49.041] [INFO ] > Starting: process_smiles [n_structures=1566425]
#> [2025-12-28 23:16:49.042] [INFO ] Processing SMILES with RDKit
#> [2025-12-28 23:16:58.380] [INFO ] Processing 400 new SMILES with RDKit
#> [2025-12-28 23:16:58.387] [INFO ] Starting SMILES processing pipeline
#> [2025-12-28 23:16:58.387] [INFO ] Input: /tmp/Rtmp9oDSfr/file2176660bb40b.smi
#> [2025-12-28 23:16:58.387] [INFO ] Output: /tmp/Rtmp9oDSfr/file21766c229c7b.csv.gz
#> [2025-12-28 23:16:58.387] [INFO ] Input file validated: /tmp/Rtmp9oDSfr/file2176660bb40b.smi
#> [2025-12-28 23:16:58.387] [INFO ] Output file validated: /tmp/Rtmp9oDSfr/file21766c229c7b.csv.gz
#> [2025-12-28 23:16:58.387] [INFO ] Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> [2025-12-28 23:16:58.387] [INFO ] SMILES supplier initialized
#> [23:16:58] Explicit valence for atom # 1 N, 3, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 386
#> [23:16:58] ERROR: Explicit valence for atom # 1 N, 3, is greater than permitted
#> [23:16:58] Explicit valence for atom # 0 P, 11, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 389
#> [23:16:58] ERROR: Explicit valence for atom # 0 P, 11, is greater than permitted
#> [23:16:58] Explicit valence for atom # 21 N, 4, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 390
#> [23:16:58] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
#> [23:16:58] Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 391
#> [23:16:58] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [23:16:58] Explicit valence for atom # 6 C, 5, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 392
#> [23:16:58] ERROR: Explicit valence for atom # 6 C, 5, is greater than permitted
#> [23:16:58] Explicit valence for atom # 18 S, 7, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 393
#> [23:16:58] ERROR: Explicit valence for atom # 18 S, 7, is greater than permitted
#> [23:16:58] 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
#> [23:16:58] SMILES Parse Error: check for mistakes around position 76:
#> [23:16:58] C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C
#> [23:16:58] ~~~~~~~~~~~~~~~~~~~~^
#> [23:16:58] 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
#> [23:16:58] SMILES Parse Error: check for mistakes around position 32:
#> [23:16:58] C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2
#> [23:16:58] ~~~~~~~~~~~~~~~~~~~~^
#> [23:16:58] 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
#> [23:16:58] SMILES Parse Error: check for mistakes around position 49:
#> [23:16:58] )\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2
#> [23:16:58] ~~~~~~~~~~~~~~~~~~~~^
#> [23:16:58] 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
#> [23:16:58] SMILES Parse Error: check for mistakes around position 66:
#> [23:16:58] )=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(
#> [23:16:58] ~~~~~~~~~~~~~~~~~~~~^
#> [23:16:58] 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'
#> [23:16:58] ERROR: Smiles parse error on line 394
#> [23:16:58] 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'
#> [23:16:58] Explicit valence for atom # 5 P, 6, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 395
#> [23:16:58] ERROR: Explicit valence for atom # 5 P, 6, is greater than permitted
#> [23:16:58] Explicit valence for atom # 0 He, 1, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 396
#> [23:16:58] ERROR: Explicit valence for atom # 0 He, 1, is greater than permitted
#> [23:16:58] Explicit valence for atom # 0 He, 1, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 397
#> [23:16:58] ERROR: Explicit valence for atom # 0 He, 1, is greater than permitted
#> [23:16:58] Explicit valence for atom # 0 He, 1, is greater than permitted
#> [23:16:58] ERROR: Could not sanitize molecule on line 398
#> [23:16:58] ERROR: Explicit valence for atom # 0 He, 1, is greater than permitted
#> [23:16:59] Explicit valence for atom # 56 P, 7, is greater than permitted
#> [2025-12-28 23:16:59.063] [WARNING] Failed to process SMILES 'CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCO[P-]([O])(=O)=O': Explicit valence for atom # 56 P, 7, is greater than permitted
#> [23:16:59] Explicit valence for atom # 4 P, 7, is greater than permitted
#> [2025-12-28 23:16:59.064] [WARNING] Failed to process SMILES '[H][C@](O)(CO[P-]([O])(=O)=O)C=O': Explicit valence for atom # 4 P, 7, is greater than permitted
#> [23:16:59] Explicit valence for atom # 7 As, 7, is greater than permitted
#> [2025-12-28 23:16:59.066] [WARNING] Failed to process SMILES 'C1=CC=C2C(=C1)O[As-]34(O2)(OC5=CC=CC=C5O3)OC6=CC=CC=C6O4': Explicit valence for atom # 7 As, 7, is greater than permitted
#> [23:16:59] Explicit valence for atom # 7 Si, 6, is greater than permitted
#> [2025-12-28 23:16:59.070] [WARNING] Failed to process SMILES 'C1COCC[NH+]1C[Si-]23(OC(C(O2)(C4=CC=CC=C4)C5=CC=CC=C5)(C6=CC=CC=C6)C7=CC=CC=C7)OC(C(O3)(C8=CC=CC=C8)C9=CC=CC=C9)(C1=CC=CC=C1)C1=CC=CC=C1': Explicit valence for atom # 7 Si, 6, is greater than permitted
#> [2025-12-28 23:16:59.090] [WARNING] Batch processing: 4/389 molecules failed
#> [2025-12-28 23:16:59.092] [INFO ] Processing complete. Total molecules processed: 385
#> [2025-12-28 23:16:59.130] [INFO ] Successfully processed 385 SMILES
#> [2025-12-28 23:17:04.471] [INFO ] [OK] Completed: process_smiles [n_processed=1500432] (15.4s)
#> [2025-12-28 23:17:19.716] [INFO ] Referenced structure-organism pairs (879,672)
#> [2025-12-28 23:17:23.871] [INFO ] Structures: 393,351 stereoisomers, 1,006,123 without stereochemistry, 1,184,186 constitutional isomers
#> [2025-12-28 23:17:43.876] [INFO ] Unique organisms (36,801)
#> [2025-12-28 23:17:43.968] [INFO ] Processing 919 organism name(s) for OTT taxonomy lookup
#> [2025-12-28 23:17:44.471] [INFO ] Querying OTT API in 10 batches
#> [2025-12-28 23:17:49.501] [INFO ] Retrieving detailed taxonomy for 13 unique OTT IDs
#> [2025-12-28 23:17:51.730] [INFO ] Got OTTaxonomy!
#> [2025-12-28 23:17:51.765] [INFO ] Exporting parameters to: data/interim/params/251228_231751_prepare_libraries_sop_merged.yaml
#> [2025-12-28 23:17:51.767] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/keys.tsv.gz, n_rows=879672]
#> [2025-12-28 23:17:52.884] [INFO ] [OK] Completed: export_output [size_bytes=17720627] (1.1s)
#> [2025-12-28 23:17:52.887] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz, n_rows=35896]
#> [2025-12-28 23:17:52.973] [INFO ] [OK] Completed: export_output [size_bytes=939193] (86ms)
#> [2025-12-28 23:17:52.975] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/structures/stereo.tsv.gz, n_rows=1401759]
#> [2025-12-28 23:17:56.317] [INFO ] [OK] Completed: export_output [size_bytes=43459608] (3.3s)
#> [2025-12-28 23:17:56.319] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/structures/metadata.tsv.gz, n_rows=1456988]
#> [2025-12-28 23:17:57.959] [INFO ] [OK] Completed: export_output [size_bytes=35902905] (1.6s)
#> [2025-12-28 23:17:57.961] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/structures/names.tsv.gz, n_rows=423004]
#> [2025-12-28 23:17:58.543] [INFO ] [OK] Completed: export_output [size_bytes=11206404] (582ms)
#> [2025-12-28 23:17:58.545] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz, n_rows=146393]
#> [2025-12-28 23:17:58.692] [INFO ] [OK] Completed: export_output [size_bytes=2492954] (147ms)
#> [2025-12-28 23:17:58.695] [INFO ] > Starting: export_output [file=data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz, n_rows=141815]
#> [2025-12-28 23:17:58.982] [INFO ] [OK] Completed: export_output [size_bytes=2395030] (287ms)
#> ✔ lib_sop_mer completed [1m 19.3s, 114.12 MB]
#> + edg_spe dispatched
#> ✔ edg_spe completed [0ms, 433.43 kB]
#> + lib_mer_str_tax_npc dispatched
#> ✔ lib_mer_str_tax_npc completed [0ms, 2.40 MB]
#> + lib_mer_str_met dispatched
#> ✔ lib_mer_str_met completed [0ms, 35.90 MB]
#> + lib_mer_str_nam dispatched
#> ✔ lib_mer_str_nam completed [0ms, 11.21 MB]
#> + lib_mer_str_stereo dispatched
#> ✔ lib_mer_str_stereo completed [0ms, 43.46 MB]
#> + lib_mer_str_tax_cla dispatched
#> ✔ lib_mer_str_tax_cla completed [0ms, 2.49 MB]
#> + lib_mer_key dispatched
#> ✔ lib_mer_key completed [0ms, 17.72 MB]
#> + lib_mer_org_tax_ott dispatched
#> ✔ lib_mer_org_tax_ott completed [1ms, 939.19 kB]
#> + ann_sir_pre dispatched
#> [2025-12-28 23:18:02.837] [INFO ] > Starting: prepare_annotations_sirius [version=6]
#> [2025-12-28 23:18:03.033] [INFO ] > Starting: complement_metadata [n_input=479]
#> [2025-12-28 23:18:24.976] [INFO ] [OK] Completed: complement_metadata [n_enriched=479] (21.9s)
#> [2025-12-28 23:18:24.985] [INFO ] [OK] Completed: prepare_annotations_sirius [n_canopus=14, n_formulas=14, n_structures=479] (22.1s)
#> [2025-12-28 23:18:25.005] [INFO ] Exporting parameters to: data/interim/params/251228_231825_prepare_annotations_sirius.yaml
#> [2025-12-28 23:18:25.007] [INFO ] > Starting: export_output [file=data/interim/annotations/example_canopusPrepared.tsv.gz, n_rows=14]
#> [2025-12-28 23:18:25.008] [INFO ] [OK] Completed: export_output [size_bytes=784] (1ms)
#> [2025-12-28 23:18:25.009] [INFO ] > Starting: export_output [file=data/interim/annotations/example_formulaPrepared.tsv.gz, n_rows=14]
#> [2025-12-28 23:18:25.011] [INFO ] [OK] Completed: export_output [size_bytes=471] (1ms)
#> [2025-12-28 23:18:25.012] [INFO ] > Starting: export_output [file=data/interim/annotations/example_siriusPrepared.tsv.gz, n_rows=479]
#> [2025-12-28 23:18:25.016] [INFO ] [OK] Completed: export_output [size_bytes=24373] (4ms)
#> ✔ ann_sir_pre completed [22.2s, 25.63 kB]
#> + ann_spe_pre dispatched
#> [2025-12-28 23:18:25.855] [INFO ] Preparing spectral matching annotations from 2 file(s)
#> [2025-12-28 23:18:31.427] [INFO ] > Starting: complement_metadata [n_input=564609]
#> [2025-12-28 23:19:02.202] [INFO ] [OK] Completed: complement_metadata [n_enriched=564609] (30.8s)
#> [2025-12-28 23:19:02.218] [INFO ] Exporting parameters to: data/interim/params/251228_231902_prepare_annotations_spectra.yaml
#> [2025-12-28 23:19:02.220] [INFO ] > Starting: export_output [file=data/interim/annotations/example_spectralMatchesPrepared.tsv.gz, n_rows=564609]
#> [2025-12-28 23:19:04.682] [INFO ] [OK] Completed: export_output [size_bytes=53145112] (2.5s)
#> ✔ ann_spe_pre completed [38.8s, 53.15 MB]
#> + ann_spe_exp_gnp_pre dispatched
#> [2025-12-28 23:19:05.564] [INFO ] > Starting: prepare_annotations_gnps [n_files=1]
#> [2025-12-28 23:19:05.565] [WARN ] No GNPS annotations found, returning an empty file instead
#> [2025-12-28 23:19:05.567] [INFO ] [OK] Completed: prepare_annotations_gnps [n_annotations=1] (4ms)
#> [2025-12-28 23:19:05.586] [INFO ] Exporting parameters to: data/interim/params/251228_231905_prepare_annotations_gnps.yaml
#> [2025-12-28 23:19:05.587] [INFO ] > Starting: export_output [file=data/interim/annotations/example_gnpsPrepared.tsv.gz, n_rows=1]
#> [2025-12-28 23:19:05.589] [INFO ] [OK] Completed: export_output [size_bytes=237] (1ms)
#> ✔ ann_spe_exp_gnp_pre completed [31ms, 237 B]
#> + ann_ms1_pre dispatched
#> [2025-12-28 23:19:05.918] [INFO ] > Starting: annotate_masses [ms_mode=pos, tolerance_ppm=10, tolerance_rt=0.02]
#> [2025-12-28 23:19:05.919] [INFO ] Starting mass-based annotation
#> [2025-12-28 23:19:05.920] [INFO ] ============================================================
#> [2025-12-28 23:19:05.921] [INFO ] Data Sanitizing: Pre-flight Checks
#> [2025-12-28 23:19:05.922] [INFO ] ============================================================
#> [2025-12-28 23:19:05.923] [INFO ] Checking features file...
#> [2025-12-28 23:19:05.959] [INFO ] [OK] Features file: 5328 rows, 5 columns
#> [2025-12-28 23:19:05.960] [INFO ] ============================================================
#> [2025-12-28 23:19:05.961] [INFO ] [OK] All pre-flight checks passed!
#> [2025-12-28 23:19:05.962] [INFO ] Data validation complete. Ready to proceed.
#> [2025-12-28 23:19:05.963] [INFO ] ============================================================
#> [2025-12-28 23:19:05.998] [INFO ] Processing 5328 features for annotation
#> [2025-12-28 23:19:22.013] [INFO ] Already 2112 adducts previously detected
#> [2025-12-28 23:19:22.015] [INFO ] > Starting: harmonize_adducts [n_rows=5328]
#> [2025-12-28 23:19:22.025] [INFO ] [OK] Completed: harmonize_adducts [n_unique_before=13, n_unique_after=13] (10ms)
#> [2025-12-28 23:19:22.084] [INFO ] Here are the top 10 observed m/z differences inside the RT windows:
#> [2025-12-28 23:19:22.086] [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
#> [2025-12-28 23:19:22.087] [INFO ] These differences may help identify potential preprocessing issues
#> [2025-12-28 23:19:25.285] [WARN ] Some adducts were unproperly detected, defaulting to (de)protonated
#> [2025-12-28 23:20:08.195] [INFO ] > Starting: decorate_masses [n_annotations=189181]
#> [2025-12-28 23:20:08.232] [INFO ] MS1 annotations: 47999 unique structures across 4232 features
#> [2025-12-28 23:20:08.233] [INFO ] [OK] Completed: decorate_masses [n_structures=47999, n_features=4232] (38ms)
#> [2025-12-28 23:20:08.283] [INFO ] Exporting parameters to: data/interim/params/251228_232008_annotate_masses.yaml
#> [2025-12-28 23:20:08.285] [INFO ] > Starting: export_output [file=data/interim/features/example_edgesMasses.tsv, n_rows=2653]
#> [2025-12-28 23:20:08.287] [INFO ] [OK] Completed: export_output [size_bytes=81706] (1ms)
#> [2025-12-28 23:20:08.288] [INFO ] > Starting: export_output [file=data/interim/annotations/example_ms1Prepared.tsv.gz, n_rows=189181]
#> [2025-12-28 23:20:09.024] [INFO ] [OK] Completed: export_output [size_bytes=10847057] (735ms)
#> [2025-12-28 23:20:09.025] [INFO ] [OK] Completed: annotate_masses [n_annotations=189181, n_edges=2653] (1m 3s)
#> ✔ ann_ms1_pre completed [1m 3.1s, 10.93 MB]
#> + tax_pre dispatched
#> [2025-12-28 23:20:09.808] [INFO ] > Starting: prepare_taxa [taxon=NULL]
#> [2025-12-28 23:20:09.964] [INFO ] Processing 2 organism name(s) for OTT taxonomy lookup
#> [2025-12-28 23:20:10.240] [INFO ] Querying OTT API in 1 batches
#> [2025-12-28 23:20:10.444] [INFO ] Retrying failed queries using genus names only
#> [2025-12-28 23:20:10.450] [INFO ] Retrying with 1 genus names: blk
#> [2025-12-28 23:20:10.653] [INFO ] Retrieving detailed taxonomy for 1 unique OTT IDs
#> [2025-12-28 23:20:10.776] [INFO ] Got OTTaxonomy!
#> [2025-12-28 23:20:11.209] [INFO ] [OK] Completed: prepare_taxa [n_features=5328] (1.4s)
#> [2025-12-28 23:20:11.239] [INFO ] Exporting parameters to: data/interim/params/251228_232011_prepare_taxa.yaml
#> [2025-12-28 23:20:11.241] [INFO ] > Starting: export_output [file=data/interim/taxa/example_taxed.tsv.gz, n_rows=5328]
#> [2025-12-28 23:20:11.249] [INFO ] [OK] Completed: export_output [size_bytes=19697] (7ms)
#> ✔ tax_pre completed [1.4s, 19.70 kB]
#> + ann_sir_pre_can dispatched
#> ✔ ann_sir_pre_can completed [0ms, 784 B]
#> + ann_sir_pre_str dispatched
#> ✔ ann_sir_pre_str completed [0ms, 24.37 kB]
#> + ann_sir_pre_for dispatched
#> ✔ ann_sir_pre_for completed [0ms, 471 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 [0ms, 10.85 MB]
#> + fea_edg_pre dispatched
#> [2025-12-28 23:20:13.241] [INFO ] > Starting: prepare_features_edges [n_edge_types=2]
#> [2025-12-28 23:20:13.277] [INFO ] [OK] Completed: prepare_features_edges [n_edges=14089] (36ms)
#> [2025-12-28 23:20:13.297] [INFO ] Exporting parameters to: data/interim/params/251228_232013_prepare_features_edges.yaml
#> [2025-12-28 23:20:13.298] [INFO ] > Starting: export_output [file=data/interim/features/example_edges.tsv, n_rows=14089]
#> [2025-12-28 23:20:13.301] [INFO ] [OK] Completed: export_output [size_bytes=637979] (3ms)
#> ✔ fea_edg_pre completed [61ms, 637.98 kB]
#> + ann_fil dispatched
#> [2025-12-28 23:20:13.622] [INFO ] > Starting: filter_annotations [n_annotation_files=4, tolerance_rt=Inf]
#> [2025-12-28 23:20:13.623] [INFO ] Filtering annotations
#> [2025-12-28 23:20:13.661] [INFO ] Processing 5328 unique features for annotation filtering
#> [2025-12-28 23:20:17.969] [INFO ] Removing MS1 annotations superseded by spectral matches
#> [2025-12-28 23:20:20.718] [INFO ] Removed 71751 redundant MS1 annotations
#> [2025-12-28 23:20:20.719] [INFO ] Total annotations before RT filtering: 682519
#> [2025-12-28 23:20:21.904] [INFO ] Filtering annotations outside Inf min RT tolerance
#> [2025-12-28 23:20:25.036] [INFO ] Removed 0 annotations based on retention time tolerance
#> [2025-12-28 23:20:25.258] [INFO ] Exporting parameters to: data/interim/params/251228_232025_filter_annotations.yaml
#> [2025-12-28 23:20:25.259] [INFO ] > Starting: export_output [file=data/interim/annotations/example_annotationsFiltered.tsv.gz, n_rows=683113]
#> [2025-12-28 23:20:27.926] [INFO ] [OK] Completed: export_output [size_bytes=51529712] (2.7s)
#> [2025-12-28 23:20:27.927] [INFO ] [OK] Completed: filter_annotations [n_filtered=683113] (14.3s)
#> ✔ ann_fil completed [14.3s, 51.53 MB]
#> + fea_com dispatched
#> [2025-12-28 23:20:28.561] [INFO ] > Starting: create_components [n_input_files=1]
#> [2025-12-28 23:20:28.562] [INFO ] Creating components from 1 edge file(s)
#> [2025-12-28 23:20:28.574] [INFO ] Loaded 12217 edges connecting 4537 unique features
#> [2025-12-28 23:20:28.582] [INFO ] Found 1481 components
#> [2025-12-28 23:20:28.593] [INFO ] Component sizes - Min: 1, Max: 2068, Mean: 3.1
#> [2025-12-28 23:20:28.608] [INFO ] Exporting parameters to: data/interim/params/251228_232028_create_components.yaml
#> [2025-12-28 23:20:28.610] [INFO ] > Starting: export_output [file=data/interim/features/example_components.tsv, n_rows=4537]
#> [2025-12-28 23:20:28.611] [INFO ] [OK] Completed: export_output [size_bytes=38686] (1ms)
#> [2025-12-28 23:20:28.612] [INFO ] Components written to: data/interim/features/example_components.tsv
#> [2025-12-28 23:20:28.613] [INFO ] [OK] Completed: create_components [n_components=1481, n_features=4537] (52ms)
#> ✔ fea_com completed [55ms, 38.69 kB]
#> + int_com dispatched
#> ✔ int_com completed [0ms, 38.69 kB]
#> + fea_com_pre dispatched
#> [2025-12-28 23:20:29.269] [INFO ] > Starting: prepare_features_components [n_files=1]
#> [2025-12-28 23:20:29.274] [INFO ] [OK] Completed: prepare_features_components [n_assignments=4537] (5ms)
#> [2025-12-28 23:20:29.290] [INFO ] Exporting parameters to: data/interim/params/251228_232029_prepare_features_components.yaml
#> [2025-12-28 23:20:29.291] [INFO ] > Starting: export_output [file=data/interim/features/example_componentsPrepared.tsv, n_rows=4537]
#> [2025-12-28 23:20:29.293] [INFO ] [OK] Completed: export_output [size_bytes=38681] (1ms)
#> ✔ fea_com_pre completed [25ms, 38.68 kB]
#> + ann_wei dispatched
#> [2025-12-28 23:20:29.618] [INFO ] Starting annotation weighting and scoring
#> [2025-12-28 23:20:29.620] [INFO ] > Starting: weight_annotations [n_candidates_neighbors=16, n_candidates_final=1]
#> [2025-12-28 23:20:45.947] [INFO ]
#> candidate_library n
#> ISDB - Wikidata 519661
#> TIMA MS1 89821
#> gnps 21563
#> merlin 20091
#> massbank 3195
#> SIRIUS 479
#> [2025-12-28 23:20:53.013] [INFO ] > Starting: weight_bio [n_annotations=639851, n_sop=881013]
#> [2025-12-28 23:20:53.015] [INFO ] Weighting 639851 annotations by biological source
#> [2025-12-28 23:20:56.952] [INFO ] [OK] Completed: weight_bio [n_weighted=639851] (3.9s)
#> [2025-12-28 23:20:56.953] [INFO ] > Starting: decorate_bio [n_annotations=639851]
#> [2025-12-28 23:20:58.217] [INFO ] Taxonomically informed metabolite annotation reranked:
#> Kingdom level: 39425 structures
#> Phylum level: 38980 structures
#> Class level: 33432 structures
#> Order level: 9156 structures
#> Family level: 7372 structures
#> Tribe level: 1239 structures
#> Genus level: 979 structures
#> Species level: 471 structures
#> Variety level: 91 structures
#> Biota level: 91 structures
#> [2025-12-28 23:20:58.218] [INFO ] [OK] Completed: decorate_bio [n_processed=639851] (1.3s)
#> [2025-12-28 23:20:58.220] [INFO ] > Starting: clean_bio [n_annotations=639851, minimal_consistency=0]
#> [2025-12-28 23:21:16.700] [INFO ] [OK] Completed: clean_bio [n_cleaned=639842] (18.5s)
#> [2025-12-28 23:21:16.701] [INFO ] > Starting: weight_chemo [n_input=639842]
#> [2025-12-28 23:21:16.702] [INFO ] Weighting 639842 annotations by chemical consistency
#> [2025-12-28 23:21:17.981] [INFO ] [OK] Completed: weight_chemo [n_weighted=639842] (1.3s)
#> [2025-12-28 23:21:17.982] [INFO ] > Starting: decorate_chemo [n_annotations=639842]
#> [2025-12-28 23:21:18.693] [INFO ] Chemically informed metabolite annotation reranked:
#> Classyfire:
#> Kingdom level: 27940 structures
#> Superclass level: 27830 structures
#> Class level: 25618 structures
#> Parent level: 19622 structures
#> NPClassifier:
#> Pathway level: 28142 structures
#> Superclass level: 27077 structures
#> Class level: 19744 structures
#> [2025-12-28 23:21:18.694] [INFO ] [OK] Completed: decorate_chemo [n_processed=639842] (711ms)
#> [2025-12-28 23:21:18.703] [INFO ] Cleaning chemically weighted annotations
#> [2025-12-28 23:21:18.704] [INFO ] Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score
#> [2025-12-28 23:21:27.537] [INFO ] Sampling candidates for 3084 features with more than 7 candidates per score
#> [2025-12-28 23:21:27.618] [INFO ] > Starting: filter_high_confidence [n_input=16958, context=filtered]
#> [2025-12-28 23:21:27.633] [INFO ] [filtered] Removed 15710 low-confidence candidates (92.6% of 16958 total)
#> [2025-12-28 23:21:27.634] [INFO ] [filtered] 1248 high-confidence candidates remaining (7.4%)
#> [2025-12-28 23:21:27.635] [INFO ] [OK] Completed: filter_high_confidence [n_filtered=1248, n_removed=15710] (17ms)
#> [2025-12-28 23:21:27.638] [INFO ] Summarizing annotation results
#> [2025-12-28 23:21:33.699] [INFO ] Annotated features: 586/5328 (11.0%)
#> [2025-12-28 23:21:33.796] [INFO ] Summarizing annotation results
#> [2025-12-28 23:21:54.681] [INFO ] Annotated features: 4733/5328 (88.8%)
#> [2025-12-28 23:21:55.262] [INFO ] [OK] Completed: weight_annotations [n_annotations=NULL] (1m 26s)
#> [2025-12-28 23:21:55.284] [INFO ] Exporting parameters to: data/processed/20251228_232155_example/251228_232155_prepare_params.yaml
#> [2025-12-28 23:21:55.305] [INFO ] Exporting parameters to: data/processed/20251228_232155_example/251228_232155_prepare_params_advanced.yaml
#> [2025-12-28 23:21:55.307] [INFO ] > Starting: export_output [file=data/processed/20251228_232155_example/example_results_mini.tsv, n_rows=5857]
#> [2025-12-28 23:21:55.310] [INFO ] [OK] Completed: export_output [size_bytes=808117] (3ms)
#> [2025-12-28 23:21:55.311] [INFO ] > Starting: export_output [file=data/processed/20251228_232155_example/example_results_filtered.tsv, n_rows=5857]
#> [2025-12-28 23:21:55.316] [INFO ] [OK] Completed: export_output [size_bytes=1767257] (5ms)
#> [2025-12-28 23:21:55.317] [INFO ] > Starting: export_output [file=data/processed/20251228_232155_example/example_results.tsv, n_rows=457649]
#> [2025-12-28 23:21:55.896] [INFO ] [OK] Completed: export_output [size_bytes=280972640] (579ms)
#> [2025-12-28 23:21:55.898] [INFO ] Results exported: example_results.tsv
#> ✔ ann_wei completed [1m 26.3s, 282.74 MB]
#> ✔ ended pipeline [20m 16.1s, 130 completed, 0 skipped]
#> There were 14 warnings (use warnings() to see them)3 Performing Taxonomically Informed Metabolite Annotation
Adriano Rutz 
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!
The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!
We hope you enjoyed using TIMA and are pleased to hear from you!
For any remark or suggestion, please fill an issue or feel free to contact us directly.
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Citation
BibTeX citation:
@online{rutz2025,
author = {Rutz, Adriano},
title = {3 {Performing} {Taxonomically} {Informed} {Metabolite}
{Annotation}},
date = {2025-12-28},
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 28, 2025. https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/III-processing.html.