3 Performing Taxonomically Informed Metabolite Annotation

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

tima::tima_full()
#> + par_def_ann_spe dispatched
#> ✔ par_def_ann_spe completed [28ms, 2.14 kB]
#> + par_def_wei_ann dispatched
#> ✔ par_def_wei_ann completed [1ms, 5.27 kB]
#> + par_def_pre_ann_gnp dispatched
#> ✔ par_def_pre_ann_gnp completed [0ms, 1.42 kB]
#> + par_def_pre_lib_sop_mer dispatched
#> ✔ par_def_pre_lib_sop_mer completed [1ms, 3.40 kB]
#> + yaml_paths dispatched
#> ✔ yaml_paths completed [1ms, 11.52 kB]
#> + par_def_pre_lib_sop_lot dispatched
#> ✔ par_def_pre_lib_sop_lot completed [1ms, 494 B]
#> + par_def_ann_mas dispatched
#> ✔ par_def_ann_mas completed [1ms, 6.09 kB]
#> + par_def_pre_lib_sop_hmd dispatched
#> ✔ par_def_pre_lib_sop_hmd completed [0ms, 492 B]
#> + par_def_fil_ann dispatched
#> ✔ par_def_fil_ann completed [1ms, 1.34 kB]
#> + par_def_pre_lib_sop_clo dispatched
#> ✔ par_def_pre_lib_sop_clo completed [1ms, 523 B]
#> + par_def_pre_lib_spe dispatched
#> ✔ par_def_pre_lib_spe completed [1ms, 1.57 kB]
#> + par_def_pre_fea_com dispatched
#> ✔ par_def_pre_fea_com completed [0ms, 358 B]
#> + par_def_cre_com dispatched
#> ✔ par_def_cre_com completed [1ms, 375 B]
#> + par_def_cre_edg_spe dispatched
#> ✔ par_def_cre_edg_spe completed [1ms, 1.42 kB]
#> + par_def_pre_fea_edg dispatched
#> ✔ par_def_pre_fea_edg completed [1ms, 706 B]
#> + par_def_pre_fea_tab dispatched
#> ✔ par_def_pre_fea_tab completed [1ms, 860 B]
#> + par_def_pre_lib_rt dispatched
#> ✔ par_def_pre_lib_rt completed [1ms, 2.20 kB]
#> + par_def_pre_ann_spe dispatched
#> ✔ par_def_pre_ann_spe completed [0ms, 1.46 kB]
#> + par_def_pre_ann_sir dispatched
#> ✔ par_def_pre_ann_sir completed [1ms, 1.93 kB]
#> + par_def_pre_tax dispatched
#> ✔ par_def_pre_tax completed [1ms, 1.51 kB]
#> + par_def_pre_lib_sop_ecm dispatched
#> ✔ par_def_pre_lib_sop_ecm completed [1ms, 492 B]
#> + paths dispatched
#> ✔ paths completed [1ms, 2.52 kB]
#> + lib_spe_exp_gnp_pre_sop dispatched
#> [2025-11-20 12:11:00.373 ] [INFO ] Downloading file from: https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz
#> [2025-11-20 12:11:00.889 ] [INFO ] Successfully downloaded 1.35 MB to: data/interim/libraries/sop/gnps_11566051_prepared.tsv.gz
#> ✔ lib_spe_exp_gnp_pre_sop completed [517ms, 1.42 MB]
#> + lib_spe_exp_mb_pre_sop dispatched
#> [2025-11-20 12:11:01.060 ] [INFO ] Downloading file from: https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/massbank_2025051_prepared.tsv.gz
#> [2025-11-20 12:11:01.209 ] [INFO ] Successfully downloaded 0.46 MB to: data/interim/libraries/sop/massbank_2025051_prepared.tsv.gz
#> ✔ lib_spe_exp_mb_pre_sop completed [151ms, 480.97 kB]
#> + lib_spe_exp_mer_pre_sop dispatched
#> [2025-11-20 12:11:01.375 ] [INFO ] Downloading file from: https://github.com/Adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/sop/merlin_13911806_prepared.tsv.gz
#> [2025-11-20 12:11:01.596 ] [INFO ] Successfully downloaded 1.14 MB to: data/interim/libraries/sop/merlin_13911806_prepared.tsv.gz
#> ✔ lib_spe_exp_mer_pre_sop completed [222ms, 1.19 MB]
#> + lib_spe_is_wik_pre_sop dispatched
#> [2025-11-20 12:11:01.766 ] [INFO ] Downloading file from: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/wikidata_spectral_5607185_prepared.tsv.gz
#> [2025-11-20 12:11:02.082 ] [INFO ] Successfully downloaded 36.15 MB to: data/interim/libraries/sop/wikidata_5607185_prepared.tsv.gz
#> ✔ lib_spe_is_wik_pre_sop completed [318ms, 37.90 MB]
#> + lib_spe_exp_mb_pre_pos dispatched
#> [2025-11-20 12:11:02.265 ] [INFO ] Downloading file from: https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/massbank_2025051_pos.rds
#> [2025-11-20 12:11:02.970 ] [INFO ] Successfully downloaded 18.51 MB to: data/interim/libraries/spectra/exp/massbank_2025051_pos.rds
#> ✔ lib_spe_exp_mb_pre_pos completed [707ms, 19.41 MB]
#> + par_pre_par dispatched
#> ✔ par_pre_par completed [0ms, 1.38 kB]
#> + lib_spe_exp_mer_pre_neg dispatched
#> [2025-11-20 12:11:03.314 ] [INFO ] Downloading file from: https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/merlin_13911806_neg.rds
#> [2025-11-20 12:11:04.150 ] [INFO ] Successfully downloaded 30.08 MB to: data/interim/libraries/spectra/exp/merlin_13911806_neg.rds
#> ✔ lib_spe_exp_mer_pre_neg completed [838ms, 31.54 MB]
#> + lib_spe_is_wik_pre_neg dispatched
#> [2025-11-20 12:11:04.336 ] [INFO ] Downloading file from: https://github.com/taxonomicallyinformedannotation/tima-isdb-neg/raw/main/wikidata_5607185_neg.rds
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#> [2025-11-20 12:11:14.223 ] [INFO ] Successfully downloaded 655.49 MB to: data/interim/libraries/spectra/is/wikidata_5607185_neg.rds
#> ✔ lib_spe_is_wik_pre_neg completed [9.9s, 687.33 MB]
#> + par_pre_par2 dispatched
#> ✔ par_pre_par2 completed [0ms, 21.49 kB]
#> + lib_spe_is_wik_pre_pos dispatched
#> [2025-11-20 12:11:14.806 ] [INFO ] Downloading file from: https://github.com/taxonomicallyinformedannotation/tima-isdb-pos/raw/main/wikidata_5607185_pos.rds
#> Downloading   7% ■■■                              12s
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#> [2025-11-20 12:11:27.034 ] [INFO ] Successfully downloaded 823.93 MB to: data/interim/libraries/spectra/is/wikidata_5607185_pos.rds
#> ✔ lib_spe_is_wik_pre_pos completed [12.2s, 863.95 MB]
#> + lib_sop_lot dispatched
#> [2025-11-20 12:11:27.514 ] [INFO ] Retrieving latest version from Zenodo: 10.5281/zenodo.5794106
#> [2025-11-20 12:11:29.905 ] [INFO ] Downloading 230106_frozen_metadata.csv.gz from https://doi.org/10.5281/zenodo.5794106 (The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata))
#> [2025-11-20 12:11:29.906 ] [INFO ] Downloading file from: https://zenodo.org/records/7534071/files/230106_frozen_metadata.csv.gz
#> [2025-11-20 12:12:06.386 ] [INFO ] Successfully downloaded 88.67 MB to: data/source/libraries/sop/lotus.csv.gz
#> ✔ lib_sop_lot completed [38.9s, 92.98 MB]
#> + lib_sop_hmd dispatched
#> [2025-11-20 12:12:06.595 ] [INFO ] Downloading file from: https://hmdb.ca/system/downloads/current/structures.zip
#> Downloading  38% ■■■■■■■■■■■■                      2s
#> Downloading  74% ■■■■■■■■■■■■■■■■■■■■■■■           1s
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#> [2025-11-20 12:12:09.724 ] [INFO ] Successfully downloaded 92.01 MB to: data/source/libraries/sop/hmdb/structures.zip
#> ✔ lib_sop_hmd completed [3.1s, 96.48 MB]
#> + lib_spe_exp_gnp_pre_neg dispatched
#> [2025-11-20 12:12:09.932 ] [INFO ] Downloading file from: https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/gnps_11566051_neg.rds
#> [2025-11-20 12:12:12.073 ] [INFO ] Successfully downloaded 146.98 MB to: data/interim/libraries/spectra/exp/gnps_11566051_neg.rds
#> ✔ lib_spe_exp_gnp_pre_neg completed [2.1s, 154.12 MB]
#> + lib_spe_exp_mer_pre_pos dispatched
#> [2025-11-20 12:12:12.308 ] [INFO ] Downloading file from: https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/merlin_13911806_pos.rds
#> [2025-11-20 12:12:13.836 ] [INFO ] Successfully downloaded 81 MB to: data/interim/libraries/spectra/exp/merlin_13911806_pos.rds
#> ✔ lib_spe_exp_mer_pre_pos completed [1.5s, 84.94 MB]
#> + lib_sop_ecm dispatched
#> [2025-11-20 12:12:14.051 ] [INFO ] Downloading file from: https://ecmdb.ca/download/ecmdb.json.zip
#> [2025-11-20 12:12:15.270 ] [INFO ] Successfully downloaded 1.27 MB to: data/source/libraries/sop/ecmdb.json.zip
#> ✔ lib_sop_ecm completed [1.2s, 1.33 MB]
#> + lib_spe_exp_mb_pre_neg dispatched
#> [2025-11-20 12:12:15.442 ] [INFO ] Downloading file from: https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/massbank_2025051_neg.rds
#> [2025-11-20 12:12:15.984 ] [INFO ] Successfully downloaded 6.73 MB to: data/interim/libraries/spectra/exp/massbank_2025051_neg.rds
#> ✔ lib_spe_exp_mb_pre_neg completed [543ms, 7.06 MB]
#> + lib_spe_exp_gnp_pre_pos dispatched
#> [2025-11-20 12:12:16.162 ] [INFO ] Downloading file from: https://github.com/adafede/SpectRalLibRaRies/raw/main/data/interim/libraries/spectra/exp/gnps_11566051_pos.rds
#> Downloading  17% ■■■■■■                            5s
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#> Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■   0s
#> [2025-11-20 12:12:22.360 ] [INFO ] Successfully downloaded 458.98 MB to: data/interim/libraries/spectra/exp/gnps_11566051_pos.rds
#> ✔ lib_spe_exp_gnp_pre_pos completed [6.2s, 481.27 MB]
#> + par_fin_par dispatched
#> ✔ par_fin_par completed [1ms, 307 B]
#> + par_fin_par2 dispatched
#> ✔ par_fin_par2 completed [2ms, 2.99 kB]
#> + par_usr_pre_lib_sop_mer dispatched
#> ✔ par_usr_pre_lib_sop_mer completed [1.4s, 1.55 kB]
#> + par_usr_pre_lib_sop_lot dispatched
#> ✔ par_usr_pre_lib_sop_lot completed [1.5s, 174 B]
#> + par_usr_pre_tax dispatched
#> ✔ par_usr_pre_tax completed [1.4s, 438 B]
#> + par_usr_pre_ann_gnp dispatched
#> ✔ par_usr_pre_ann_gnp completed [1.3s, 708 B]
#> + par_usr_pre_lib_sop_hmd dispatched
#> ✔ par_usr_pre_lib_sop_hmd completed [1.4s, 178 B]
#> + par_usr_cre_com dispatched
#> ✔ par_usr_cre_com completed [1.4s, 200 B]
#> + par_usr_pre_lib_sop_clo dispatched
#> ✔ par_usr_pre_lib_sop_clo completed [1.4s, 205 B]
#> + par_usr_cre_edg_spe dispatched
#> ✔ par_usr_cre_edg_spe completed [1.4s, 452 B]
#> + par_usr_pre_fea_com dispatched
#> ✔ par_usr_pre_fea_com completed [1.4s, 200 B]
#> + par_usr_pre_fea_edg dispatched
#> ✔ par_usr_pre_fea_edg completed [1.4s, 328 B]
#> + par_usr_pre_lib_sop_ecm dispatched
#> ✔ par_usr_pre_lib_sop_ecm completed [1.4s, 176 B]
#> + par_usr_fil_ann dispatched
#> ✔ par_usr_fil_ann completed [1.3s, 668 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_ann_spe dispatched
#> ✔ par_usr_ann_spe completed [1.4s, 1.03 kB]
#> + par_usr_pre_ann_spe dispatched
#> ✔ par_usr_pre_ann_spe completed [1.4s, 731 B]
#> + par_usr_pre_lib_spe dispatched
#> ✔ par_usr_pre_lib_spe completed [1.3s, 298 B]
#> + par_usr_pre_ann_sir dispatched
#> ✔ par_usr_pre_ann_sir completed [1.4s, 900 B]
#> + par_usr_ann_mas dispatched
#> ✔ par_usr_ann_mas completed [1.4s, 2.68 kB]
#> + par_usr_wei_ann dispatched
#> ✔ par_usr_wei_ann completed [1.3s, 1.78 kB]
#> + par_pre_lib_sop_mer dispatched
#> ✔ par_pre_lib_sop_mer completed [1ms, 558 B]
#> + par_pre_lib_sop_lot dispatched
#> ✔ par_pre_lib_sop_lot completed [1ms, 186 B]
#> + par_pre_tax dispatched
#> ✔ par_pre_tax completed [1ms, 330 B]
#> + par_pre_ann_gnp dispatched
#> ✔ par_pre_ann_gnp completed [0ms, 336 B]
#> + par_pre_lib_sop_hmd dispatched
#> ✔ par_pre_lib_sop_hmd completed [1ms, 191 B]
#> + par_cre_com dispatched
#> ✔ par_cre_com completed [1ms, 191 B]
#> + par_pre_lib_sop_clo dispatched
#> ✔ par_pre_lib_sop_clo completed [0ms, 213 B]
#> + par_cre_edg_spe dispatched
#> ✔ par_cre_edg_spe completed [1ms, 389 B]
#> + par_pre_fea_com dispatched
#> ✔ par_pre_fea_com completed [1ms, 184 B]
#> + par_pre_fea_edg dispatched
#> ✔ par_pre_fea_edg completed [0ms, 244 B]
#> + par_pre_lib_sop_ecm dispatched
#> ✔ par_pre_lib_sop_ecm completed [1ms, 191 B]
#> + par_fil_ann dispatched
#> ✔ par_fil_ann completed [1ms, 346 B]
#> + par_pre_fea_tab dispatched
#> ✔ par_pre_fea_tab completed [1ms, 278 B]
#> + par_pre_lib_rt dispatched
#> ✔ par_pre_lib_rt completed [0ms, 375 B]
#> + par_ann_spe dispatched
#> ✔ par_ann_spe completed [1ms, 497 B]
#> + par_pre_ann_spe dispatched
#> ✔ par_pre_ann_spe completed [1ms, 334 B]
#> + par_pre_lib_spe dispatched
#> ✔ par_pre_lib_spe completed [0ms, 404 B]
#> + par_pre_ann_sir dispatched
#> ✔ par_pre_ann_sir completed [1ms, 405 B]
#> + par_ann_mas dispatched
#> ✔ par_ann_mas completed [1ms, 1.13 kB]
#> + par_wei_ann dispatched
#> ✔ par_wei_ann completed [1ms, 952 B]
#> + lib_sop_mer_str_pro dispatched
#> [2025-11-20 12:12:57.673 ] [INFO ] Downloading file from: https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/processed.csv.gz
#> [2025-11-20 12:12:58.248 ] [INFO ] Successfully downloaded 86.32 MB to: data/interim/libraries/sop/merged/structures/processed.csv.gz
#> ✔ lib_sop_mer_str_pro completed [576ms, 90.51 MB]
#> + lib_sop_lot_pre dispatched
#> [2025-11-20 12:12:58.459 ] [INFO ] Loading LOTUS database from: data/source/libraries/sop/lotus.csv.gz
#> [2025-11-20 12:13:09.361 ] [INFO ] Prepared 791809 unique structure-organism pairs from LOTUS
#> [2025-11-20 12:13:09.363 ] [INFO ] Exporting data to: data/interim/libraries/sop/lotus_prepared.tsv.gz
#> [2025-11-20 12:13:12.840 ] [INFO ] Successfully exported 791809 rows to data/interim/libraries/sop/lotus_prepared.tsv.gz
#> ✔ lib_sop_lot_pre completed [14.4s, 46.52 MB]
#> + lib_sop_hmd_pre dispatched
#> [2025-11-20 12:13:13.217 ] [INFO ] Preparing HMDB structure-organism pairs
#> [2025-11-20 12:13:57.468 ] [INFO ] Exporting data to: data/interim/libraries/sop/hmdb_prepared.tsv.gz
#> [2025-11-20 12:13:58.071 ] [INFO ] Successfully exported 217776 rows to data/interim/libraries/sop/hmdb_prepared.tsv.gz
#> ✔ lib_sop_hmd_pre completed [44.9s, 8.06 MB]
#> + lib_sop_clo_pre dispatched
#> [2025-11-20 12:13:58.622 ] [INFO ] Preparing closed structure-organism pairs library
#> [2025-11-20 12:13:58.626 ] [WARN ] Closed resource not accessible at: ~/Git/lotus-processor/data/processed/240412_closed_metadata.csv.gz. Returning empty template instead.
#> [2025-11-20 12:13:58.642 ] [INFO ] Exporting parameters to: data/interim/params/251120_121358_prepare_libraries_sop_closed.yaml
#> [2025-11-20 12:13:58.643 ] [INFO ] Exporting data to: data/interim/libraries/sop/closed_prepared.tsv.gz
#> [2025-11-20 12:13:58.644 ] [INFO ] Successfully exported 1 rows to data/interim/libraries/sop/closed_prepared.tsv.gz
#> ✔ lib_sop_clo_pre completed [23ms, 273 B]
#> + lib_sop_ecm_pre dispatched
#> [2025-11-20 12:13:58.869 ] [INFO ] Preparing ECMDB structure-organism pairs
#> [2025-11-20 12:13:59.496 ] [INFO ] Exporting parameters to: data/interim/params/251120_121359_prepare_libraries_sop_ecmdb.yaml
#> [2025-11-20 12:13:59.497 ] [INFO ] Exporting data to: data/interim/libraries/sop/ecmdb_prepared.tsv.gz
#> [2025-11-20 12:13:59.512 ] [INFO ] Successfully exported 3760 rows to data/interim/libraries/sop/ecmdb_prepared.tsv.gz
#> ✔ lib_sop_ecm_pre completed [645ms, 177.47 kB]
#> + par_pre_fea_tab_fil_fea_raw dispatched
#> ✔ par_pre_fea_tab_fil_fea_raw completed [0ms, 451.55 kB]
#> + lib_rt dispatched
#> [2025-11-20 12:13:59.916 ] [INFO ] Preparing retention time libraries
#> [2025-11-20 12:13:59.927 ] [WARN ] No retention time library found, returning empty retention time and sop tables.
#> [2025-11-20 12:13:59.969 ] [INFO ] Exporting parameters to: data/interim/params/251120_121359_prepare_libraries_rt.yaml
#> [2025-11-20 12:13:59.970 ] [INFO ] Exporting data to: data/interim/libraries/rt/prepared.tsv.gz
#> [2025-11-20 12:13:59.971 ] [INFO ] Successfully exported 1 rows to data/interim/libraries/rt/prepared.tsv.gz
#> [2025-11-20 12:13:59.973 ] [INFO ] Exporting data to: data/interim/libraries/sop/rt_prepared.tsv.gz
#> [2025-11-20 12:13:59.974 ] [INFO ] Successfully exported 1 rows to data/interim/libraries/sop/rt_prepared.tsv.gz
#> ✔ lib_rt completed [60ms, 191 B]
#> + par_ann_spe_fil_spe_raw dispatched
#> ✔ par_ann_spe_fil_spe_raw completed [0ms, 7.77 MB]
#> + lib_spe_exp_int_pre dispatched
#> [2025-11-20 12:14:00.365 ] [INFO ] Preparing spectral libraries
#> [2025-11-20 12:14:00.370 ] [WARN ] Your input file does not exist, returning empty lib instead.
#> [2025-11-20 12:14:01.601 ] [INFO ] Exporting data to: data/interim/libraries/sop/internal_prepared.tsv.gz
#> [2025-11-20 12:14:01.602 ] [INFO ] Successfully exported 1 rows to data/interim/libraries/sop/internal_prepared.tsv.gz
#> [2025-11-20 12:14:01.702 ] [INFO ] Exporting parameters to: data/interim/params/251120_121401_prepare_libraries_spectra.yaml
#> ✔ lib_spe_exp_int_pre completed [1.3s, 155 B]
#> + input_features dispatched
#> ✔ input_features completed [1ms, 451.55 kB]
#> + lib_rt_sop dispatched
#> ✔ lib_rt_sop completed [1ms, 105 B]
#> + lib_rt_rts dispatched
#> ✔ lib_rt_rts completed [0ms, 86 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]
#> + fea_pre dispatched
#> [2025-11-20 12:14:04.236 ] [INFO ] Preparing features table from: data/source/example_features.csv
#> [2025-11-20 12:14:04.330 ] [INFO ] Prepared 5328 feature-sample pairs
#> [2025-11-20 12:14:04.353 ] [INFO ] Exporting parameters to: data/interim/params/251120_121404_prepare_features_tables.yaml
#> [2025-11-20 12:14:04.354 ] [INFO ] Exporting data to: data/interim/features/example_features.tsv.gz
#> [2025-11-20 12:14:04.367 ] [INFO ] Successfully exported 5328 rows to data/interim/features/example_features.tsv.gz
#> ✔ fea_pre completed [154ms, 95.63 kB]
#> + fea_edg_spe dispatched
#> [2025-11-20 12:14:04.679 ] [INFO ] Creating spectral similarity network edges
#> [2025-11-20 12:14:04.680 ] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-11-20 12:14:04.706 ] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-11-20 12:14:06.513 ] [INFO ] Processed 10000 spectra...
#> [2025-11-20 12:14:07.779 ] [INFO ] Total spectra read: 16282
#> [2025-11-20 12:14:14.181 ] [INFO ] Loaded 16282 spectra from file
#> [2025-11-20 12:14:16.434 ] [INFO ] Sanitizing 4087 spectra (cutoff: 0)
#> [2025-11-20 12:14:16.452 ] [INFO ] Sanitization complete: 3840/4087 spectra retained (94%, 247 removed)
#> [2025-11-20 12:14:16.453 ] [INFO ] Import complete: 3840 spectra ready for analysis
#> [2025-11-20 12:14:16.455 ] [INFO ] =============================================
#> [2025-11-20 12:14:16.456 ] [INFO ] = Take yourself a break, you deserve it.    =
#> [2025-11-20 12:14:16.457 ] [INFO ] =============================================
#> [2025-11-20 12:20:04.414 ] [INFO ] Created 9223 edges passing thresholds
#> [2025-11-20 12:20:04.484 ] [INFO ] Exporting parameters to: data/interim/params/251120_122004_create_edges_spectra.yaml
#> [2025-11-20 12:20:04.485 ] [INFO ] Exporting data to: data/interim/features/example_edgesSpectra.tsv
#> [2025-11-20 12:20:04.488 ] [INFO ] Successfully exported 11577 rows to data/interim/features/example_edgesSpectra.tsv
#> ✔ fea_edg_spe completed [5m 59.8s, 533.82 kB]
#> + lib_sop_mer dispatched
#> [2025-11-20 12:20:04.826 ] [INFO ] Preparing merged structure-organism pairs library
#> [2025-11-20 12:20:20.484 ] [INFO ] Splitting concatenated SOP library into standardized components
#> [2025-11-20 12:20:24.899 ] [INFO ] Processing SMILES strings with RDKit
#> Downloading uv...Done!
#> Downloading cpython-3.12.12-linux-x86_64-gnu (download) (30.9MiB)
#>  Downloading cpython-3.12.12-linux-x86_64-gnu (download)
#> Downloading numpy (15.8MiB)
#> Downloading pillow (6.7MiB)
#> Downloading rdkit (34.5MiB)
#>  Downloading pillow
#>  Downloading numpy
#>  Downloading rdkit
#> Installed 3 packages in 29ms
#> [2025-11-20 12:20:39.017 ] [INFO ] Processing 61 new SMILES with RDKit
#> 2025-11-20 12:20:39,019 - __main__ - INFO - Starting SMILES processing pipeline
#> 2025-11-20 12:20:39,019 - __main__ - INFO - Input: /tmp/Rtmp4ViNU1/file1eec3272663d.smi
#> 2025-11-20 12:20:39,019 - __main__ - INFO - Output: /tmp/Rtmp4ViNU1/file1eec764dccce.csv.gz
#> 2025-11-20 12:20:39,019 - __main__ - INFO - Input file validated: /tmp/Rtmp4ViNU1/file1eec3272663d.smi
#> 2025-11-20 12:20:39,019 - __main__ - INFO - Output file validated: /tmp/Rtmp4ViNU1/file1eec764dccce.csv.gz
#> 2025-11-20 12:20:39,019 - __main__ - INFO - Processing parameters: workers=8, batch_size=1000, progress_interval=10000
#> 2025-11-20 12:20:39,019 - __main__ - INFO - SMILES supplier initialized
#> [12:20:39] Explicit valence for atom # 1 N, 3, is greater than permitted
#> [12:20:39] ERROR: Could not sanitize molecule on line 1
#> [12:20:39] ERROR: Explicit valence for atom # 1 N, 3, is greater than permitted
#> [12:20:39] Explicit valence for atom # 0 P, 11, is greater than permitted
#> [12:20:39] ERROR: Could not sanitize molecule on line 2
#> [12:20:39] ERROR: Explicit valence for atom # 0 P, 11, is greater than permitted
#> [12:20:39] Explicit valence for atom # 21 N, 4, is greater than permitted
#> [12:20:39] ERROR: Could not sanitize molecule on line 3
#> [12:20:39] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
#> [12:20:39] Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [12:20:39] ERROR: Could not sanitize molecule on line 4
#> [12:20:39] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than permitted
#> [12:20:39] Explicit valence for atom # 6 C, 5, is greater than permitted
#> [12:20:39] ERROR: Could not sanitize molecule on line 5
#> [12:20:39] ERROR: Explicit valence for atom # 6 C, 5, is greater than permitted
#> [12:20:39] Explicit valence for atom # 18 S, 7, is greater than permitted
#> [12:20:39] ERROR: Could not sanitize molecule on line 6
#> [12:20:39] ERROR: Explicit valence for atom # 18 S, 7, is greater than permitted
#> [12:20:39] 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
#> [12:20:39] SMILES Parse Error: check for mistakes around position 76:
#> [12:20:39] C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(O)=CC=C1)C
#> [12:20:39] ~~~~~~~~~~~~~~~~~~~~^
#> [12:20:39] 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
#> [12:20:39] SMILES Parse Error: check for mistakes around position 32:
#> [12:20:39] C1)C-1=C2\CCC(=N2)\C(=C2/N\C(\C=C2)=C(/C2
#> [12:20:39] ~~~~~~~~~~~~~~~~~~~~^
#> [12:20:39] 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
#> [12:20:39] SMILES Parse Error: check for mistakes around position 49:
#> [12:20:39] )\C(=C2/N\C(\C=C2)=C(/C2=N/C(/C=C2)=C(\C2
#> [12:20:39] ~~~~~~~~~~~~~~~~~~~~^
#> [12:20:39] 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
#> [12:20:39] SMILES Parse Error: check for mistakes around position 66:
#> [12:20:39] )=C(/C2=N/C(/C=C2)=C(\C2=CC=C\-1N2)C1=CC(
#> [12:20:39] ~~~~~~~~~~~~~~~~~~~~^
#> [12:20:39] 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'
#> [12:20:39] ERROR: Smiles parse error on line 7
#> [12:20:39] 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'
#> 2025-11-20 12:20:39,075 - __main__ - INFO - Processing complete. Total molecules processed: 54
#> [2025-11-20 12:20:39.105 ] [INFO ] Successfully processed 54 SMILES
#> [2025-11-20 12:21:01.832 ] [INFO ] Led to 877903 referenced structure-organism pairs
#> [2025-11-20 12:21:04.529 ] [INFO ] Corresponding to 393389 unique stereoisomers (excluding structures without stereochemistry)...
#> [2025-11-20 12:21:06.305 ] [INFO ] ... and 1007790 unique structures without stereochemistry...
#> [2025-11-20 12:21:06.394 ] [INFO ] ... or 1184311 unique constitutional isomers (ignoring stereochemistry)
#> [2025-11-20 12:21:26.730 ] [INFO ] ... among 36800 unique organisms
#> [2025-11-20 12:21:26.821 ] [INFO ] Processing 919 organism name(s) for OTT taxonomy lookup
#> [2025-11-20 12:21:27.244 ] [INFO ] Querying OTT API in 10 batches
#> [2025-11-20 12:21:30.668 ] [INFO ] Retrieving detailed taxonomy for 13 unique OTT IDs
#> [2025-11-20 12:21:32.227 ] [INFO ] Got OTTaxonomy!
#> [2025-11-20 12:21:32.261 ] [INFO ] Exporting parameters to: data/interim/params/251120_122132_prepare_libraries_sop_merged.yaml
#> [2025-11-20 12:21:32.262 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/keys.tsv.gz
#> [2025-11-20 12:21:33.443 ] [INFO ] Successfully exported 877903 rows to data/interim/libraries/sop/merged/keys.tsv.gz
#> [2025-11-20 12:21:33.444 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz
#> [2025-11-20 12:21:33.534 ] [INFO ] Successfully exported 35894 rows to data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz
#> [2025-11-20 12:21:33.535 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/structures/stereo.tsv.gz
#> [2025-11-20 12:21:37.017 ] [INFO ] Successfully exported 1404391 rows to data/interim/libraries/sop/merged/structures/stereo.tsv.gz
#> [2025-11-20 12:21:37.019 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/structures/metadata.tsv.gz
#> [2025-11-20 12:21:38.673 ] [INFO ] Successfully exported 1458341 rows to data/interim/libraries/sop/merged/structures/metadata.tsv.gz
#> [2025-11-20 12:21:38.675 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/structures/names.tsv.gz
#> [2025-11-20 12:21:39.272 ] [INFO ] Successfully exported 423199 rows to data/interim/libraries/sop/merged/structures/names.tsv.gz
#> [2025-11-20 12:21:39.273 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz
#> [2025-11-20 12:21:39.425 ] [INFO ] Successfully exported 146393 rows to data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz
#> [2025-11-20 12:21:39.427 ] [INFO ] Exporting data to: data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz
#> [2025-11-20 12:21:39.727 ] [INFO ] Successfully exported 141818 rows to data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz
#> ✔ lib_sop_mer completed [1m 34.9s, 250 B]
#> + ann_spe_pos dispatched
#> [2025-11-20 12:21:40.836 ] [INFO ] Starting spectral annotation in pos mode
#> [2025-11-20 12:21:40.840 ] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-11-20 12:21:40.841 ] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-11-20 12:21:42.542 ] [INFO ] Processed 10000 spectra...
#> [2025-11-20 12:21:43.783 ] [INFO ] Total spectra read: 16282
#> [2025-11-20 12:21:49.357 ] [INFO ] Loaded 16282 spectra from file
#> [2025-11-20 12:21:50.169 ] [INFO ] Sanitizing 4087 spectra (cutoff: 0)
#> [2025-11-20 12:21:50.281 ] [INFO ] Sanitization complete: 3840/4087 spectra retained (94%, 247 removed)
#> [2025-11-20 12:21:50.282 ] [INFO ] Import complete: 3840 spectra ready for analysis
#> [2025-11-20 12:21:50.284 ] [INFO ] Importing spectra from: data/interim/libraries/spectra/is/wikidata_5607185_pos.rds
#> [2025-11-20 12:22:08.875 ] [INFO ] Loaded 998198 spectra from file
#> [2025-11-20 12:22:09.540 ] [INFO ] Import complete: 998198 spectra ready for analysis
#> [2025-11-20 12:22:09.541 ] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/internal_pos.rds
#> [2025-11-20 12:22:09.542 ] [INFO ] Loaded 1 spectra from file
#> [2025-11-20 12:22:09.544 ] [INFO ] Import complete: 0 spectra ready for analysis
#> [2025-11-20 12:22:09.544 ] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/gnps_11566051_pos.rds
#> [2025-11-20 12:22:15.102 ] [INFO ] Loaded 354789 spectra from file
#> [2025-11-20 12:22:15.290 ] [INFO ] Import complete: 354788 spectra ready for analysis
#> [2025-11-20 12:22:15.291 ] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/massbank_2025051_pos.rds
#> [2025-11-20 12:22:15.987 ] [INFO ] Loaded 66388 spectra from file
#> [2025-11-20 12:22:16.043 ] [INFO ] Import complete: 66388 spectra ready for analysis
#> [2025-11-20 12:22:16.044 ] [INFO ] Importing spectra from: data/interim/libraries/spectra/exp/merlin_13911806_pos.rds
#> [2025-11-20 12:22:20.813 ] [INFO ] Loaded 208280 spectra from file
#> [2025-11-20 12:22:20.966 ] [INFO ] Import complete: 208273 spectra ready for analysis
#> [2025-11-20 12:22:36.130 ] [INFO ]          library spectra unique_connectivities
#>  ISDB - Wikidata  998198                998198
#>             gnps  354788                 22675
#>           merlin  208273                 26197
#>         massbank   66388                  5901
#> [2025-11-20 12:22:37.499 ] [INFO ] Calculating entropy and similarity for 3840 spectra
#> [2025-11-20 12:27:23.697 ] [INFO ] 321348 Candidates were annotated on 3679 features, with at least 0 similarity score.
#> [2025-11-20 12:27:23.730 ] [INFO ] Exporting parameters to: data/interim/params/251120_122723_annotate_spectra.yaml
#> [2025-11-20 12:27:23.732 ] [INFO ] Exporting data to: data/interim/annotations/example_spectralMatches_pos.tsv.gz
#> [2025-11-20 12:27:25.518 ] [INFO ] Successfully exported 629774 rows to data/interim/annotations/example_spectralMatches_pos.tsv.gz
#> ✔ ann_spe_pos completed [5m 44.7s, 37.54 MB]
#> + ann_spe_neg dispatched
#> [2025-11-20 12:27:26.889 ] [INFO ] Starting spectral annotation in neg mode
#> [2025-11-20 12:27:26.896 ] [INFO ] Importing spectra from: data/source/example_spectra.mgf
#> [2025-11-20 12:27:26.941 ] [INFO ] Reading MGF file (7.41 MB) with optimized parser: data/source/example_spectra.mgf
#> [2025-11-20 12:27:28.612 ] [INFO ] Processed 10000 spectra...
#> [2025-11-20 12:27:29.822 ] [INFO ] Total spectra read: 16282
#> [2025-11-20 12:27:34.968 ] [INFO ] Loaded 16282 spectra from file
#> [2025-11-20 12:27:34.982 ] [WARN ] No spectra to sanitize
#> [2025-11-20 12:27:34.983 ] [INFO ] Import complete: 0 spectra ready for analysis
#> [2025-11-20 12:27:34.984 ] [WARN ] No query spectra loaded; returning empty dataframe
#> [2025-11-20 12:27:35.017 ] [INFO ] Exporting parameters to: data/interim/params/251120_122735_annotate_spectra.yaml
#> [2025-11-20 12:27:35.018 ] [INFO ] Exporting data to: data/interim/annotations/example_spectralMatches_neg.tsv.gz
#> [2025-11-20 12:27:35.020 ] [INFO ] Successfully exported 1 rows to data/interim/annotations/example_spectralMatches_neg.tsv.gz
#> ✔ ann_spe_neg completed [8.1s, 187 B]
#> + edg_spe dispatched
#> ✔ edg_spe completed [0ms, 533.82 kB]
#> + lib_mer_key dispatched
#> ✔ lib_mer_key completed [1ms, 18.06 MB]
#> + lib_mer_str_met dispatched
#> ✔ lib_mer_str_met completed [0ms, 36.02 MB]
#> + lib_mer_str_nam dispatched
#> ✔ lib_mer_str_nam completed [0ms, 11.28 MB]
#> + lib_mer_str_stereo dispatched
#> ✔ lib_mer_str_stereo completed [0ms, 43.58 MB]
#> + lib_mer_str_tax_cla dispatched
#> ✔ lib_mer_str_tax_cla completed [0ms, 2.51 MB]
#> + lib_mer_str_tax_npc dispatched
#> ✔ lib_mer_str_tax_npc completed [0ms, 2.44 MB]
#> + lib_mer_org_tax_ott dispatched
#> ✔ lib_mer_org_tax_ott completed [0ms, 939.13 kB]
#> + ann_ms1_pre dispatched
#> [2025-11-20 12:27:38.497 ] [INFO ] Starting mass-based annotation in pos mode
#> [2025-11-20 12:27:38.533 ] [INFO ] Processing 5328 features for annotation
#> [2025-11-20 12:27:59.970 ] [INFO ] Already 2112 adducts previously detected
#> [2025-11-20 12:28:00.034 ] [INFO ] Here are the top 10 observed m/z differences inside the RT windows:
#> [2025-11-20 12:28:00.035 ] [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
#> [2025-11-20 12:28:00.036 ] [INFO ] These differences may help identify potential preprocessing issues
#> [2025-11-20 12:28:39.436 ] [INFO ] MS1 annotation results: 48099 unique structures annotated across 4224 features
#> [2025-11-20 12:28:39.484 ] [INFO ] Exporting parameters to: data/interim/params/251120_122839_annotate_masses.yaml
#> [2025-11-20 12:28:39.485 ] [INFO ] Exporting data to: data/interim/features/example_edgesMasses.tsv
#> [2025-11-20 12:28:39.486 ] [INFO ] Successfully exported 2653 rows to data/interim/features/example_edgesMasses.tsv
#> [2025-11-20 12:28:39.487 ] [INFO ] Exporting data to: data/interim/annotations/example_ms1Prepared.tsv.gz
#> [2025-11-20 12:28:40.218 ] [INFO ] Successfully exported 187762 rows to data/interim/annotations/example_ms1Prepared.tsv.gz
#> ✔ ann_ms1_pre completed [1m 1.7s, 157 B]
#> + ann_spe_exp_gnp_pre dispatched
#> [2025-11-20 12:28:41.010 ] [INFO ] Preparing GNPS annotations
#> [2025-11-20 12:28:41.013 ] [WARN ] No GNPS annotations found, returning an empty file instead
#> [2025-11-20 12:28:41.031 ] [INFO ] Exporting parameters to: data/interim/params/251120_122841_prepare_annotations_gnps.yaml
#> [2025-11-20 12:28:41.032 ] [INFO ] Exporting data to: data/interim/annotations/example_gnpsPrepared.tsv.gz
#> [2025-11-20 12:28:41.033 ] [INFO ] Successfully exported 1 rows to data/interim/annotations/example_gnpsPrepared.tsv.gz
#> ✔ ann_spe_exp_gnp_pre completed [23ms, 237 B]
#> + ann_spe_pre dispatched
#> [2025-11-20 12:28:41.410 ] [INFO ] Preparing spectral matching annotations from 2 file(s)
#> [2025-11-20 12:29:18.375 ] [INFO ] Exporting parameters to: data/interim/params/251120_122918_prepare_annotations_spectra.yaml
#> [2025-11-20 12:29:18.377 ] [INFO ] Exporting data to: data/interim/annotations/example_spectralMatchesPrepared.tsv.gz
#> [2025-11-20 12:29:21.220 ] [INFO ] Successfully exported 629774 rows to data/interim/annotations/example_spectralMatchesPrepared.tsv.gz
#> ✔ ann_spe_pre completed [39.8s, 61.25 MB]
#> + ann_sir_pre dispatched
#> [2025-11-20 12:29:22.221 ] [INFO ] Preparing SIRIUS 6 annotations
#> [2025-11-20 12:29:40.210 ] [INFO ] Exporting parameters to: data/interim/params/251120_122940_prepare_annotations_sirius.yaml
#> [2025-11-20 12:29:40.211 ] [INFO ] Exporting data to: data/interim/annotations/example_canopusPrepared.tsv.gz
#> [2025-11-20 12:29:40.212 ] [INFO ] Successfully exported 14 rows to data/interim/annotations/example_canopusPrepared.tsv.gz
#> [2025-11-20 12:29:40.213 ] [INFO ] Exporting data to: data/interim/annotations/example_formulaPrepared.tsv.gz
#> [2025-11-20 12:29:40.214 ] [INFO ] Successfully exported 16 rows to data/interim/annotations/example_formulaPrepared.tsv.gz
#> [2025-11-20 12:29:40.215 ] [INFO ] Exporting data to: data/interim/annotations/example_siriusPrepared.tsv.gz
#> [2025-11-20 12:29:40.219 ] [INFO ] Successfully exported 479 rows to data/interim/annotations/example_siriusPrepared.tsv.gz
#> ✔ ann_sir_pre completed [18s, 165 B]
#> + tax_pre dispatched
#> [2025-11-20 12:29:41.416 ] [INFO ] Preparing taxonomic assignments for features
#> [2025-11-20 12:29:41.420 ] [INFO ] Using metadata for organism assignments
#> [2025-11-20 12:29:41.573 ] [INFO ] Processing 2 organism name(s) for OTT taxonomy lookup
#> [2025-11-20 12:29:41.813 ] [INFO ] Querying OTT API in 1 batches
#> [2025-11-20 12:29:42.040 ] [INFO ] Retrying failed queries using genus names only
#> [2025-11-20 12:29:42.045 ] [INFO ] Retrying with 1 genus names: blk
#> [2025-11-20 12:29:42.244 ] [INFO ] Retrieving detailed taxonomy for 1 unique OTT IDs
#> [2025-11-20 12:29:42.364 ] [INFO ] Got OTTaxonomy!
#> [2025-11-20 12:29:42.791 ] [INFO ] Exporting parameters to: data/interim/params/251120_122942_prepare_taxa.yaml
#> [2025-11-20 12:29:42.792 ] [INFO ] Exporting data to: data/interim/taxa/example_taxed.tsv.gz
#> [2025-11-20 12:29:42.799 ] [INFO ] Successfully exported 5328 rows to data/interim/taxa/example_taxed.tsv.gz
#> ✔ tax_pre completed [1.4s, 19.70 kB]
#> + ann_ms1_pre_edg dispatched
#> ✔ ann_ms1_pre_edg completed [0ms, 81.71 kB]
#> + ann_ms1_pre_ann dispatched
#> ✔ ann_ms1_pre_ann completed [0ms, 10.81 MB]
#> + ann_sir_pre_can dispatched
#> ✔ ann_sir_pre_can completed [1ms, 784 B]
#> + ann_sir_pre_for dispatched
#> ✔ ann_sir_pre_for completed [0ms, 487 B]
#> + ann_sir_pre_str dispatched
#> ✔ ann_sir_pre_str completed [0ms, 24.42 kB]
#> + fea_edg_pre dispatched
#> [2025-11-20 12:29:44.810 ] [INFO ] Preparing molecular network edges
#> [2025-11-20 12:29:44.844 ] [INFO ] Prepared 17751 total edges
#> [2025-11-20 12:29:44.862 ] [INFO ] Exporting parameters to: data/interim/params/251120_122944_prepare_features_edges.yaml
#> [2025-11-20 12:29:44.863 ] [INFO ] Exporting data to: data/interim/features/example_edges.tsv
#> [2025-11-20 12:29:44.866 ] [INFO ] Successfully exported 17751 rows to data/interim/features/example_edges.tsv
#> ✔ fea_edg_pre completed [57ms, 758.28 kB]
#> + ann_fil dispatched
#> [2025-11-20 12:29:45.193 ] [INFO ] Filtering annotations
#> [2025-11-20 12:29:45.230 ] [INFO ] Processing 5328 unique features for annotation filtering
#> [2025-11-20 12:29:49.909 ] [INFO ] Removing MS1 annotations superseded by spectral matches
#> [2025-11-20 12:29:53.017 ] [INFO ] Removed 79186 redundant MS1 annotations
#> [2025-11-20 12:29:53.018 ] [INFO ] Total annotations before RT filtering: 738830
#> [2025-11-20 12:29:54.158 ] [INFO ] Filtering annotations outside Inf min RT tolerance
#> [2025-11-20 12:29:56.817 ] [INFO ] Removed 0 annotations based on retention time tolerance
#> [2025-11-20 12:29:57.066 ] [INFO ] Exporting parameters to: data/interim/params/251120_122957_filter_annotations.yaml
#> [2025-11-20 12:29:57.067 ] [INFO ] Exporting data to: data/interim/annotations/example_annotationsFiltered.tsv.gz
#> [2025-11-20 12:30:00.022 ] [INFO ] Successfully exported 739349 rows to data/interim/annotations/example_annotationsFiltered.tsv.gz
#> ✔ ann_fil completed [14.8s, 56.22 MB]
#> + fea_com dispatched
#> [2025-11-20 12:30:00.816 ] [INFO ] Creating components from 1 edge file(s)
#> [2025-11-20 12:30:00.830 ] [INFO ] Loaded 15234 edges connecting 5909 unique features
#> [2025-11-20 12:30:00.841 ] [INFO ] Found 2513 components
#> [2025-11-20 12:30:00.860 ] [INFO ] Component sizes - Min: 1, Max: 1586, Mean: 2.4
#> [2025-11-20 12:30:00.875 ] [INFO ] Exporting parameters to: data/interim/params/251120_123000_create_components.yaml
#> [2025-11-20 12:30:00.876 ] [INFO ] Exporting data to: data/interim/features/example_components.tsv
#> [2025-11-20 12:30:00.877 ] [INFO ] Successfully exported 5909 rows to data/interim/features/example_components.tsv
#> [2025-11-20 12:30:00.878 ] [INFO ] Components written to: data/interim/features/example_components.tsv
#> ✔ fea_com completed [63ms, 51.39 kB]
#> + int_com dispatched
#> ✔ int_com completed [0ms, 51.39 kB]
#> + fea_com_pre dispatched
#> [2025-11-20 12:30:01.553 ] [INFO ] Preparing molecular network components from 1 file(s)
#> [2025-11-20 12:30:01.557 ] [INFO ] Prepared 5909 unique feature-component assignments
#> [2025-11-20 12:30:01.572 ] [INFO ] Exporting parameters to: data/interim/params/251120_123001_prepare_features_components.yaml
#> [2025-11-20 12:30:01.573 ] [INFO ] Exporting data to: data/interim/features/example_componentsPrepared.tsv
#> [2025-11-20 12:30:01.574 ] [INFO ] Successfully exported 5909 rows to data/interim/features/example_componentsPrepared.tsv
#> ✔ fea_com_pre completed [22ms, 51.38 kB]
#> + ann_pre dispatched
#> [2025-11-20 12:30:01.913 ] [INFO ] Starting annotation weighting and scoring
#> [2025-11-20 12:30:19.472 ] [INFO ]  candidate_library      n
#>    ISDB - Wikidata 577751
#>           TIMA MS1  82324
#>               gnps  25161
#>             merlin  23150
#>           massbank   3591
#>             SIRIUS    479
#> [2025-11-20 12:30:26.600 ] [INFO ] Weighting 695299 annotations by biological source
#> [2025-11-20 12:30:32.058 ] [INFO ] Taxonomically informed metabolite annotation reranked:
#> Kingdom level: 41238 structures
#> Phylum level:  40784 structures
#> Class level:   35057 structures
#> Order level:   9353 structures
#> Family level:  7515 structures
#> Tribe level:   1184 structures
#> Genus level:   919 structures
#> Species level: 402 structures
#> Variety level: 0 structures
#> [2025-11-20 12:30:47.489 ] [INFO ] Weighting 695285 annotations by chemical consistency
#> [2025-11-20 12:30:51.377 ] [INFO ] Chemically informed metabolite annotation reranked:
#> Classyfire:
#>   Kingdom level:    72980 structures
#>   Superclass level: 72946 structures
#>   Class level:      71293 structures
#>   Parent level:     67979 structures
#> NPClassifier:
#>   Pathway level:    76290 structures
#>   Superclass level: 75535 structures
#>   Class level:      71204 structures
#> [2025-11-20 12:30:51.381 ] [INFO ] Cleaning chemically weighted annotations
#> [2025-11-20 12:30:51.382 ] [INFO ] Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score
#> [2025-11-20 12:30:58.518 ] [INFO ] [filtered] Removed 20161 low-confidence candidates (92.1% of 21884 total)
#> [2025-11-20 12:30:58.519 ] [INFO ] [filtered] 1723 high-confidence candidates remaining (7.9%)
#> [2025-11-20 12:30:58.522 ] [INFO ] Summarizing annotation results
#> [2025-11-20 12:31:07.964 ] [INFO ] Summarizing annotation results
#> [2025-11-20 12:32:00.646 ] [INFO ] Exporting parameters to: data/processed/20251120_123200_example/251120_123200_prepare_params.yaml
#> [2025-11-20 12:32:00.666 ] [INFO ] Exporting parameters to: data/processed/20251120_123200_example/251120_123200_prepare_params_advanced.yaml
#> [2025-11-20 12:32:00.668 ] [INFO ] Exporting data to: data/processed/20251120_123200_example/example_results_mini.tsv
#> [2025-11-20 12:32:00.671 ] [INFO ] Successfully exported 5824 rows to data/processed/20251120_123200_example/example_results_mini.tsv
#> [2025-11-20 12:32:00.672 ] [INFO ] Exporting data to: data/processed/20251120_123200_example/example_results_filtered.tsv
#> [2025-11-20 12:32:00.677 ] [INFO ] Successfully exported 5824 rows to data/processed/20251120_123200_example/example_results_filtered.tsv
#> [2025-11-20 12:32:00.678 ] [INFO ] Exporting data to: data/processed/20251120_123200_example/example_results.tsv
#> [2025-11-20 12:32:01.465 ] [INFO ] Successfully exported 695221 rows to data/processed/20251120_123200_example/example_results.tsv
#> ✔ ann_pre completed [1m 59.6s, 371.33 MB]
#> ✔ ended pipeline [21m 6.5s, 126 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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