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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GNU General Public License v3.0
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gapfilling issues with tetracosane medium #163

Closed danfrks closed 1 year ago

danfrks commented 1 year ago

Dear developers,

I am runnig gapfill on media with specific carbon sources, such as cpd25825 (tetracosane) and cpd00618 (naphthalene).

However, the resulting xml files do not have the above metabolites after gapfilling, even though the output of gapseq fill shows some biomass flux when using the specific media. I would appreciate any insight as to why this might be the case.

A side note: I see from the output that the xml file is patched. Just to confirm, does this also apply to the RDS file?

Example medium (c-source is the last row):

compounds name maxFlux
cpd00013 NH3 100
cpd00011 CO2 10
cpd00001 H2O 100
cpd00007 O2 10
cpd00009 Phosphate 100
cpd00030 Mn2 100
cpd00034 Zn2 100
cpd00048 Sulfate 100
cpd00058 Cu2 100
cpd00063 Ca2 100
cpd00067 H 100
cpd00099 Cl- 100
cpd00149 Co2 100
cpd00205 K 100
cpd00254 Mg 100
cpd00531 Hg2 100
cpd00971 Na 100
cpd01012 Cd2 100
cpd01048 Arsenate 100
cpd10515 Fe2 100
cpd10516 fe3 100
cpd11595 chromate 100
cpd25825 tetracosane 1000

Example output:

Loading model files maxbin.001.fasta.contigs.RDS using media file cpd25825.csv

  1. Initial gapfilling: Make model grow on given media using all reactions

  2. Biomass gapfilling using core reactions only

    1 / 70 2 / 70 3 / 70 4 / 70 5 / 70 6 / 70 7 / 70 8 / 70 9 / 70 10 / 70 11 / 70 12 / 70 13 / 70 14 / 70 15 / 70 16 / 70 17 / 70 18 / 70 19 / 70 20 / 70 21 / 70 22 / 70 23 / 70 24 / 70 25 / 70 26 / 70 27 / 70 28 / 70 29 / 70 30 / 70 31 / 70 32 / 70 33 / 70 34 / 70 35 / 70 36 / 70 37 / 70 38 / 70 39 / 70 40 / 70 41 / 70 42 / 70 43 / 70 44 / 70 45 / 70 46 / 70 47 / 70 48 / 70 49 / 70 50 / 70 51 / 70 Try to gapfill ACP-c0

    52 / 70 53 / 70 54 / 70 55 / 70 56 / 70 57 / 70 58 / 70 59 / 70 60 / 70 61 / 70 Try to gapfill Calomide

    62 / 70 63 / 70 64 / 70 65 / 70 66 / 70 67 / 70 68 / 70 69 / 70 70 / 70 Try to gapfill Peptidoglycan polymer (n subunits)

Gapfill summary: Filled components: 0 ( ) Added reactions: 0 Final growth rate: 0.05147239

2b. Anaerobic biomass gapfilling using core reactions only

1 / 70 2 / 70 Try to gapfill TPP-c0

3 / 70 4 / 70 5 / 70 6 / 70 7 / 70 8 / 70 9 / 70 10 / 70 11 / 70 12 / 70 13 / 70 14 / 70 15 / 70 16 / 70 17 / 70 18 / 70 19 / 70 20 / 70 Try to gapfill Heme-c0

21 / 70 22 / 70 23 / 70 24 / 70 25 / 70 26 / 70 27 / 70 28 / 70 29 / 70 30 / 70 31 / 70 Try to gapfill L-Tyrosine-c0

32 / 70 33 / 70 34 / 70 35 / 70 36 / 70 37 / 70 38 / 70 39 / 70 40 / 70 41 / 70 42 / 70 43 / 70 44 / 70 45 / 70 46 / 70 47 / 70 48 / 70 49 / 70 50 / 70 51 / 70 Try to gapfill ACP-c0

52 / 70 53 / 70 54 / 70 55 / 70 56 / 70 57 / 70 58 / 70 59 / 70 60 / 70 61 / 70 Try to gapfill Calomide

62 / 70 63 / 70 64 / 70 65 / 70 66 / 70 67 / 70 68 / 70 69 / 70 70 / 70 Try to gapfill Peptidoglycan polymer (n subunits)

Gapfill summary: Filled components: 0 ( ) Added reactions: 0 Final growth rate: 0.05147239

  1. Energy source gapfilling with core reactions only

    1 / 351 2 / 351 3 / 351 4 / 351 5 / 351 6 / 351 7 / 351 8 / 351 9 / 351 10 / 351 11 / 351 12 / 351 13 / 351 14 / 351 15 / 351 16 / 351 17 / 351 18 / 351 19 / 351 20 / 351 21 / 351 22 / 351 23 / 351 24 / 351 25 / 351 26 / 351 27 / 351 28 / 351 29 / 351 30 / 351 31 / 351 32 / 351 33 / 351 34 / 351 35 / 351 36 / 351 37 / 351 38 / 351 39 / 351 40 / 351 41 / 351 42 / 351 43 / 351 44 / 351 45 / 351 46 / 351 47 / 351 48 / 351 49 / 351 50 / 351 51 / 351 52 / 351 53 / 351 54 / 351 55 / 351 56 / 351 57 / 351 58 / 351 59 / 351 60 / 351 61 / 351 62 / 351 63 / 351 64 / 351 65 / 351 66 / 351 67 / 351 68 / 351 69 / 351 70 / 351 71 / 351 72 / 351 73 / 351 74 / 351 75 / 351 76 / 351 77 / 351 78 / 351 79 / 351 80 / 351 81 / 351 82 / 351 83 / 351 84 / 351 85 / 351 86 / 351 87 / 351 88 / 351 89 / 351 90 / 351 91 / 351 92 / 351 93 / 351 94 / 351 95 / 351 96 / 351 97 / 351 98 / 351 99 / 351 100 / 351 101 / 351 102 / 351 103 / 351 104 / 351 105 / 351 106 / 351 107 / 351 108 / 351 109 / 351 110 / 351 111 / 351 112 / 351 113 / 351 114 / 351 115 / 351 116 / 351 117 / 351 118 / 351 119 / 351 120 / 351 121 / 351 122 / 351 123 / 351 124 / 351 125 / 351 126 / 351 127 / 351 128 / 351 129 / 351 130 / 351 131 / 351 132 / 351 133 / 351 134 / 351 135 / 351 136 / 351 137 / 351 138 / 351 139 / 351 140 / 351 141 / 351 142 / 351 143 / 351 144 / 351 145 / 351 146 / 351 147 / 351 148 / 351 149 / 351 150 / 351 151 / 351 152 / 351 153 / 351 154 / 351 155 / 351 156 / 351 157 / 351 158 / 351 159 / 351 160 / 351 161 / 351 162 / 351 163 / 351 164 / 351 165 / 351 166 / 351 167 / 351 168 / 351 169 / 351 170 / 351 171 / 351 172 / 351 173 / 351 174 / 351 175 / 351 176 / 351 177 / 351 178 / 351 179 / 351 180 / 351 181 / 351 182 / 351 183 / 351 184 / 351 185 / 351 186 / 351 187 / 351 188 / 351 189 / 351 190 / 351 191 / 351 192 / 351 193 / 351 194 / 351 195 / 351 196 / 351 197 / 351 198 / 351 199 / 351 200 / 351 201 / 351 202 / 351 203 / 351 204 / 351 205 / 351 206 / 351 207 / 351 208 / 351 209 / 351 210 / 351 211 / 351 212 / 351 213 / 351 214 / 351 215 / 351 216 / 351 217 / 351 218 / 351 219 / 351 220 / 351 221 / 351 222 / 351 223 / 351 224 / 351 225 / 351 226 / 351 227 / 351 228 / 351 229 / 351 230 / 351 231 / 351 232 / 351 233 / 351 234 / 351 235 / 351 236 / 351 237 / 351 238 / 351 239 / 351 240 / 351 241 / 351 242 / 351 243 / 351 244 / 351 245 / 351 246 / 351 247 / 351 248 / 351 249 / 351 250 / 351 251 / 351 252 / 351 253 / 351 254 / 351 255 / 351 256 / 351 257 / 351 258 / 351 259 / 351 260 / 351 261 / 351 262 / 351 263 / 351 264 / 351 265 / 351 266 / 351 267 / 351 268 / 351 269 / 351 270 / 351 271 / 351 272 / 351 273 / 351 274 / 351 275 / 351 276 / 351 277 / 351 278 / 351 279 / 351 280 / 351 281 / 351 282 / 351 283 / 351 284 / 351 285 / 351 286 / 351 287 / 351 288 / 351 289 / 351 290 / 351 291 / 351 292 / 351 293 / 351 294 / 351 295 / 351 296 / 351 297 / 351 298 / 351 299 / 351 300 / 351 301 / 351 302 / 351 303 / 351 304 / 351 305 / 351 306 / 351 307 / 351 308 / 351 309 / 351 310 / 351 311 / 351 312 / 351 313 / 351 314 / 351 315 / 351 316 / 351 317 / 351 318 / 351 319 / 351 320 / 351 321 / 351 322 / 351 323 / 351 324 / 351 325 / 351 326 / 351 327 / 351 328 / 351 329 / 351 330 / 351 331 / 351 332 / 351 333 / 351 334 / 351 335 / 351 336 / 351 337 / 351 338 / 351 339 / 351 340 / 351 341 / 351 342 / 351 343 / 351 344 / 351 345 / 351 346 / 351 347 / 351 348 / 351 349 / 351 350 / 351 351 / 351 Gapfill summary: Filled components: 0 ( ) Added reactions: 178 Final growth rate: 0.05147239

  2. Checking for potential metabolic products with core reactions only

    1 / 351 2 / 351 3 / 351 Try to gapfill D-Glucose-e0 EX_cpd00027_e0

    4 / 351 5 / 351 6 / 351 7 / 351 8 / 351 Try to gapfill Sulfate-e0 EX_cpd00048_e0

    9 / 351 10 / 351 11 / 351 12 / 351 13 / 351 Try to gapfill Choline-e0 EX_cpd00098_e0

    14 / 351 15 / 351 Try to gapfill Galactose-e0 EX_cpd00108_e0

    16 / 351 17 / 351 18 / 351 19 / 351 20 / 351 Try to gapfill Xylose-e0 EX_cpd00154_e0

    21 / 351 22 / 351 23 / 351 Try to gapfill Maltose-e0 EX_cpd00179_e0

    24 / 351 Try to gapfill Taurine-e0 EX_cpd00210_e0

    25 / 351 Try to gapfill L-Arabinose-e0 EX_cpd00224_e0

    26 / 351 Try to gapfill Ni2+-e0 EX_cpd00244_e0

    27 / 351 28 / 351 Try to gapfill H2S2O3-e0 EX_cpd00268_e0

    29 / 351 30 / 351 Try to gapfill BET-e0 EX_cpd00540_e0

    31 / 351 Try to gapfill Ferrichrome-e0 EX_cpd03724_e0

    32 / 351 33 / 351 34 / 351 35 / 351 36 / 351 37 / 351 38 / 351 39 / 351 40 / 351 41 / 351 42 / 351 43 / 351 44 / 351 45 / 351 46 / 351 47 / 351 Try to gapfill NH3-e0 EX_cpd00013_e0

    48 / 351 49 / 351 50 / 351 51 / 351 52 / 351 Try to gapfill Arsenite-e0 EX_cpd04098_e0

    53 / 351 54 / 351 55 / 351 56 / 351 Try to gapfill chromate-e0 EX_cpd11595_e0

    57 / 351 58 / 351 59 / 351 Try to gapfill D-Fructose-e0 EX_cpd00082_e0

    60 / 351 61 / 351 62 / 351 Try to gapfill GLUM-e0 EX_cpd00276_e0

    63 / 351 Try to gapfill D-Glucarate-e0 EX_cpd00609_e0

    64 / 351 65 / 351 66 / 351 67 / 351 Try to gapfill LACT-e0 EX_cpd00208_e0

    68 / 351 Try to gapfill L-Lactate-e0 EX_cpd00159_e0

    69 / 351 Try to gapfill Amylotriose-e0 EX_cpd01262_e0

    70 / 351 Try to gapfill D-Mannitol-e0 EX_cpd00314_e0

    71 / 351 72 / 351 Try to gapfill Puromycin-e0 EX_cpd01132_e0

    73 / 351 Try to gapfill L-Rhamnose-e0 EX_cpd00396_e0

    74 / 351 75 / 351 76 / 351 77 / 351 Try to gapfill Allantoin-e0 EX_cpd01092_e0

    78 / 351 Try to gapfill L-Fucose-e0 EX_cpd00751_e0

    79 / 351 80 / 351 81 / 351 Try to gapfill Decanoate-e0 EX_cpd01107_e0

    82 / 351 Try to gapfill ddca-e0 EX_cpd01741_e0

    83 / 351 Try to gapfill Myristic acid-e0 EX_cpd03847_e0

    84 / 351 Try to gapfill tetradecenoate-e0 EX_cpd15298_e0

    85 / 351 Try to gapfill Palmitate-e0 EX_cpd00214_e0

    86 / 351 Try to gapfill hexadecenoate-e0 EX_cpd15237_e0

    87 / 351 Try to gapfill ocdca-e0 EX_cpd01080_e0

    88 / 351 Try to gapfill octadecenoate-e0 EX_cpd15269_e0

    89 / 351 Try to gapfill Hexanoate-e0 EX_cpd01113_e0

    90 / 351 Try to gapfill octanoate-e0 EX_cpd03846_e0

    91 / 351 Try to gapfill D-Galactonate-e0 EX_cpd00653_e0

    92 / 351 Try to gapfill Hg2+-e0 EX_cpd00531_e0

    93 / 351 Try to gapfill Maltotetraose-e0 EX_cpd01399_e0

    94 / 351 95 / 351 96 / 351 Try to gapfill BIOT-e0 EX_cpd00104_e0

    97 / 351 98 / 351 Try to gapfill Pb-e0 EX_cpd04097_e0

    99 / 351 Try to gapfill D-Arabinose-e0 EX_cpd00185_e0

    100 / 351 101 / 351 Try to gapfill Maltoheptaose-e0 EX_cpd15494_e0

    102 / 351 Try to gapfill TRHL-e0 EX_cpd00794_e0

    103 / 351 Try to gapfill Maltodextrin-e0 EX_cpd11976_e0

    104 / 351 105 / 351 Try to gapfill Benzoate-e0 EX_cpd00153_e0

    106 / 351 Try to gapfill Itaconate-e0 EX_cpd00380_e0

    107 / 351 Try to gapfill Cytochrome c3+-e0 EX_cpd00109_e0

    108 / 351 Try to gapfill Ubiquinol-8-e0 EX_cpd15561_e0

    109 / 351 Try to gapfill Cytochrome c2+-e0 EX_cpd00110_e0

    110 / 351 Try to gapfill Ubiquinone-8-e0 EX_cpd15560_e0

    111 / 351 112 / 351 Try to gapfill mql7-e0 EX_cpd11451_e0

    113 / 351 Try to gapfill Menaquinone 7-e0 EX_cpd11606_e0

    114 / 351 Try to gapfill methymenaquinol 7-e0 EX_cpd17026_e0

    115 / 351 Try to gapfill methylmenaquinone 7-e0 EX_cpd17027_e0

    116 / 351 Try to gapfill Arsenate-e0 EX_cpd01048_e0

    117 / 351 Try to gapfill D-Mannose-e0 EX_cpd00138_e0

    118 / 351 Try to gapfill Deoxycholate-e0 EX_cpd02733_e0

    119 / 351 Try to gapfill beta-Lactose-e0 EX_cpd01354_e0

    120 / 351 Try to gapfill Lacto-N-biose-e0 EX_cpd03808_e0

    121 / 351 Try to gapfill Cellulose-e0 EX_cpd11746_e0

    122 / 351 123 / 351 Try to gapfill Cellotetraose-e0 EX_cpd01376_e0

    124 / 351 125 / 351 126 / 351 127 / 351 Try to gapfill Propionate-e0 EX_cpd00141_e0

    128 / 351 Try to gapfill (R)-1,2-Propanediol-e0 EX_cpd01861_e0

    129 / 351 Try to gapfill 1,2-Propanediol-e0 EX_cpd00453_e0

    130 / 351 131 / 351 Try to gapfill HCN-e0 EX_cpd00150_e0

    132 / 351 Try to gapfill DMSO-e0 EX_cpd08021_e0

    133 / 351 Try to gapfill Methyl sulfide-e0 EX_cpd00450_e0

    134 / 351 135 / 351 Try to gapfill Formaldehyde-e0 EX_cpd00055_e0

    136 / 351 137 / 351 138 / 351 139 / 351 140 / 351 141 / 351 Try to gapfill Nitrous oxide-e0 EX_cpd00659_e0

    142 / 351 143 / 351 144 / 351 Try to gapfill (CH3)3NO-e0 EX_cpd00811_e0

    145 / 351 Try to gapfill Methane-e0 EX_cpd01024_e0

    146 / 351 Try to gapfill CO-e0 EX_cpd00204_e0

    147 / 351 Try to gapfill Methanol-e0 EX_cpd00116_e0

    148 / 351 149 / 351 Try to gapfill hn-e0 EX_cpd11632_e0

    150 / 351 Try to gapfill n-Butanol-e0 EX_cpd03662_e0

    151 / 351 Try to gapfill Acetone-e0 EX_cpd00178_e0

    152 / 351 Try to gapfill 1,3-Propanediol-e0 EX_cpd01618_e0

    153 / 351 154 / 351 155 / 351 156 / 351 157 / 351 158 / 351 159 / 351 160 / 351 161 / 351 162 / 351 163 / 351 164 / 351 165 / 351 166 / 351 167 / 351 168 / 351 169 / 351 170 / 351 171 / 351 172 / 351 173 / 351 174 / 351 175 / 351 176 / 351 177 / 351 178 / 351 179 / 351 180 / 351 Try to gapfill Lactulose-e0 EX_cpd04349_e0

    181 / 351 Try to gapfill Melibiose-e0 EX_cpd03198_e0

    182 / 351 Try to gapfill Melitose-e0 EX_cpd00382_e0

    183 / 351 184 / 351 Try to gapfill Sucrose-e0 EX_cpd00076_e0

    185 / 351 Try to gapfill cpd20885[e0] EX_cpd20885_e0

    186 / 351 Try to gapfill Xylitol-e0 EX_cpd00306_e0

    187 / 351 188 / 351 189 / 351 190 / 351 Try to gapfill Carnitine-e0 EX_cpd00266_e0

    191 / 351 192 / 351 193 / 351 194 / 351 195 / 351 196 / 351 Try to gapfill cpd00160[e0] EX_cpd00160_e0

    197 / 351 198 / 351 Try to gapfill D-Galacturonate-e0 EX_cpd00280_e0

    199 / 351 200 / 351 Try to gapfill Glucuronate-e0 EX_cpd00164_e0

    201 / 351 202 / 351 203 / 351 204 / 351 Try to gapfill Neu5Ac-e0 EX_cpd00232_e0

    205 / 351 Try to gapfill 4-Hydroxyphenylacetate-e0 EX_cpd00489_e0

    206 / 351 207 / 351 208 / 351 Try to gapfill Nitrate-e0 EX_cpd00209_e0

    209 / 351 210 / 351 Try to gapfill FAD-e0 EX_cpd00015_e0

    211 / 351 212 / 351 213 / 351 214 / 351 215 / 351 Try to gapfill L-Ascorbate-e0 EX_cpd00059_e0

    216 / 351 217 / 351 218 / 351 219 / 351 220 / 351 221 / 351 222 / 351 223 / 351 224 / 351 225 / 351 226 / 351 227 / 351 228 / 351 229 / 351 230 / 351 231 / 351 232 / 351 233 / 351 234 / 351 235 / 351 236 / 351 237 / 351 238 / 351 239 / 351 240 / 351 241 / 351 242 / 351 Try to gapfill Folate-e0 EX_cpd00393_e0

    243 / 351 244 / 351 245 / 351 246 / 351 247 / 351 248 / 351 249 / 351 250 / 351 251 / 351 252 / 351 253 / 351 254 / 351 255 / 351 256 / 351 257 / 351 258 / 351 259 / 351 260 / 351 261 / 351 262 / 351 Try to gapfill gamma-butyrobetaine-e0 EX_cpd00870_e0

    263 / 351 Try to gapfill Cyanate-e0 EX_cpd01015_e0

    264 / 351 265 / 351 266 / 351 Try to gapfill Stachyose-e0 EX_cpd01133_e0

    267 / 351 Try to gapfill Cadaverine-e0 EX_cpd01155_e0

    268 / 351 269 / 351 270 / 351 271 / 351 272 / 351 273 / 351 274 / 351 275 / 351 276 / 351 277 / 351 278 / 351 279 / 351 280 / 351 281 / 351 282 / 351 283 / 351 Try to gapfill Vitamin B12-e0 EX_cpd03424_e0

    284 / 351 285 / 351 286 / 351 287 / 351 288 / 351 289 / 351 290 / 351 291 / 351 292 / 351 293 / 351 294 / 351 295 / 351 Try to gapfill crotonobetaine-e0 EX_cpd08305_e0

    296 / 351 297 / 351 298 / 351 299 / 351 300 / 351 301 / 351 302 / 351 303 / 351 304 / 351 305 / 351 306 / 351 307 / 351 308 / 351 309 / 351 310 / 351 311 / 351 312 / 351 313 / 351 314 / 351 315 / 351 316 / 351 317 / 351 318 / 351 319 / 351 320 / 351 321 / 351 322 / 351 323 / 351 324 / 351 325 / 351 326 / 351 327 / 351 328 / 351 329 / 351 330 / 351 331 / 351 332 / 351 333 / 351 334 / 351 335 / 351 336 / 351 337 / 351 338 / 351 339 / 351 340 / 351 341 / 351 342 / 351 Try to gapfill cpd11683[e0] EX_cpd11683_e0

    343 / 351 344 / 351 345 / 351 346 / 351 347 / 351 Try to gapfill Cholate-e0 EX_cpd00526_e0

    348 / 351 Try to gapfill Chenodiol-e0 EX_cpd01663_e0

    349 / 351 350 / 351 351 / 351 Gapfill summary: Filled components: 0 ( ) Added reactions: 0 Final growth rate: 0.05147239

Uptake at limit: O2:10

Top 10 produced metabolites: H2O:23.717, H+:16.762, N2:8.172, EX cpd11416 c0:0.051, 5-Methylthio-D-ribose:0 Patching file maxbin.001.fasta.contigs.xml ... done

danfrks commented 1 year ago

In addition, I have trouble with gapseq adapt as well:

I adapt the model using a number of carbon sources. This actually adds the metabolites (although compartment of metabolite_e0 is "NA" instead of "e0".

The problem here is that the adapted model does not grow (flux 0) when solving with cobrapy and using the metabolite as the sole carbon source. I wasn't sure what the gapfilling medium was during adapt (tried to check but my R is limited), so I moved on to gapseq fill. Netiher is working at the moment.

danfrks commented 1 year ago

Here is the (suspicious) terminal output of gapseq adapt: (for 2 parallel runs). I manually confirmed, there are no reactions ivolving these metabolites in the patched xml file, apart from an exchange reaction.

Warning in .local(model, ...) : 'lb' and 'ub' are signed different, set reversible to 'TRUE' Warning in .local(model, ...) : 'lb' and 'ub' are signed different, set reversible to 'TRUE' Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd25825 tetracosane Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00127 Phenol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00604 4-Coumarate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd25311 3-Hydroxy-4-methoxybenzaldehyde Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00153 Benzoate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00093 Anthranilate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01059 Ferulate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00561 Vanillin Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04073 Vanillate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd12715 E-Coniferyl alcohol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01400 Phenylalanine Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00881 Caffeate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00077 Catechol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00197 Protocatechuate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd25825 tetracosane Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00127 Phenol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00426 Homogentisate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00604 4-Coumarate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00489 4-Hydroxyphenylacetate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd25311 3-Hydroxy-4-methoxybenzaldehyde Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00153 Benzoate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00374 Tyramine Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00093 Anthranilate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01059 Ferulate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03982 p-Cymene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00561 Vanillin Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03987 2,3-Dihydroxy-p-cumate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04073 Vanillate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd12715 E-Coniferyl alcohol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03985 p-Cumate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01400 Phenylalanine Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00881 Caffeate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00618 Naphthalene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00077 Catechol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00197 Protocatechuate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01034 Toluol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00426 Homogentisate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01007 Benzene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00489 4-Hydroxyphenylacetate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00374 Tyramine Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04383 Ethylenzene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03982 p-Cymene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03987 2,3-Dihydroxy-p-cumate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03994 Biphenyl Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03985 p-Cumate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01617 1-Phenylethylamine Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00618 Naphthalene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01034 Toluol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04384 1-Phenylethanol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01007 Benzene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04383 Ethylenzene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00599 SALC Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03994 Biphenyl Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00153 Benzoate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01617 1-Phenylethylamine Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04384 1-Phenylethanol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00136 4-Hydroxybenzoate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00599 SALC Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00153 Benzoate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00604 4-Coumarate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00136 4-Hydroxybenzoate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd00604 4-Coumarate Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04358 Styrene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04358 Styrene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd09801 2-Methylnaphthalene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd09801 2-Methylnaphthalene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03982 p-Cymene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd03982 p-Cymene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04136 p-Xylene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04446 m-Xylene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04136 p-Xylene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04450 o-Xylene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04446 m-Xylene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01042 p-Cresol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd27783 phenanthrene-ring Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd04450 o-Xylene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd10034 Pyrene Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd01042 p-Cresol Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd27783 phenanthrene-ring Warning in add_growth(mod.out, add.met.id = sub.id, weights = rxn.weights.file, : Model is already growing with cpd10034 Pyrene Wrote file maxbin.001.fasta.contigs-adapt.xml Wrote file maxbin.002.fasta.contigs-adapt.xml

Waschina commented 1 year ago

Hi @danfrks

I am afraid that tertracosane (cpd25825) cannot yet be used as a carbon source in gapseq models. I will check which reactions might need to be added to the gapseq biochemistry database.

The growth you observe (~0.05 h-1) is likely due to ammonia oxidation and CO2 as a carbon source. The pathways and reactions for this are probably gapfilled since the medium does not allow other options.

Waschina commented 1 year ago

Do you know if there are microbial pathways known that can degrade tetracosane? gapseq builds mainly on the database knowledge of MetaCyc and ModelSEED, which both do not have reactions/pathways for tetracosane degradation.

https://modelseed.org/biochem/compounds/cpd25825 https://biocyc.org/compound?orgid=META&id=CPD-9764#tab=RXNS

danfrks commented 1 year ago

Hi @Waschina

Thanks for looking into this for me. I now realise that long alkane are not in the gapseq database. They are metabolised by long chain alkane hydroxylases ladA. I ended up manually expanding the fatty acid beta oxidation pathways and creating the relevant alkane oxidase reactions.

However I still have issues with adapt. I will post a reproducible example next week when I get some time to look at this again.

Many thanks for your reply!

danfrks commented 10 months ago

Hi,

May I reopen this thread. Apologies about copying in the error messages like that in my original post.

I'm after some advice regarding gapfilling on aromatic hydrocarbons. You've previously pointed out that the required reactions are not in the gapseq database (also in issue #101). Although, many of the metabolites (and some of the reactions) are.

Which database file does gapseq use in it /dat/? Would expanding this database resolve my gap-filling issues?

And finally, in your opinion could I pull the relevant reactions from MetaCyc (if not in modelSEED) or KEGG?

I appreciate this is a practical and not a technical question. And finally, thank you for this tool, I am coming back to it again to finish an old project. Your work is much appreciated!

Waschina commented 10 months ago

Hi @danfrks

Can you point me to the exact reactions you would like to see in Gapseq? You can provide any link (ModelSeed, KEGG, Rhea, ...).