GetOrganelle v1.7.5

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.9.7 | packaged by conda-forge | (default, Sep 14 2021, 01:17:55)  [GCC 9.4.0]
PLATFORM: Linux shilab 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.5; numpy 1.21.2; sympy 1.8; scipy 1.7.1
DEPENDENCIES: Bowtie2 2.4.4; SPAdes 3.13.0; Blast 2.6.0
GETORG_PATH=/public1/user/lisen/.GetOrganelle
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /public1/user/lisen/bruguiera_genome/bruguiera_phylogeny/bpa
/public1/user/lisen/software/miniconda2/envs/getorganelle/bin/get_organelle_from_reads.py -1 read_1.clean.fq.gz -2 read_2.clean.fq.gz -t 10 -o organelle6 -F embplant_pt --max-reads inf --reduce-reads-for-coverage inf -R 100 -k 13,21,33,45,65,85 -s ref.fa --disentangle-time-limit 10800

2021-09-23 10:50:05,964 - INFO: Pre-reading fastq ...
2021-09-23 10:50:05,965 - INFO: Unzipping reads file: read_1.clean.fq.gz (20674389674 bytes)
2021-09-23 11:02:27,361 - INFO: Unzipping reads file: read_2.clean.fq.gz (20802886293 bytes)
2021-09-23 11:15:26,949 - INFO: Counting read qualities ...
2021-09-23 11:15:27,640 - INFO: Identified quality encoding format = Sanger
2021-09-23 11:15:27,640 - INFO: Phred offset = 33
2021-09-23 11:15:27,642 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2021-09-23 11:15:27,727 - INFO: Mean error rate = 0.0018
2021-09-23 11:15:27,728 - INFO: Counting read lengths ...
2021-09-23 11:29:03,180 - INFO: Mean = 95.9 bp, maximum = 100 bp.
2021-09-23 11:29:03,181 - INFO: Reads used = 270750327+270750327
2021-09-23 11:29:03,181 - INFO: Pre-reading fastq finished.

2021-09-23 11:29:03,181 - INFO: Making seed reads ...
2021-09-23 11:29:03,230 - INFO: Making seed - bowtie2 index ...
2021-09-23 11:29:04,014 - INFO: Making seed - bowtie2 index finished.
2021-09-23 11:29:04,015 - INFO: Mapping reads to seed bowtie2 index ...
2021-09-23 12:12:42,309 - INFO: Mapping finished.
2021-09-23 12:12:42,310 - INFO: Seed reads made: organelle6/seed/embplant_pt.initial.fq (6886836355 bytes)
2021-09-23 12:12:42,325 - INFO: Making seed reads finished.

2021-09-23 12:12:42,325 - INFO: Checking seed reads and parameters ...
2021-09-23 12:12:42,325 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2021-09-23 12:12:42,325 - INFO: If the result graph is not a circular organelle genome, 
2021-09-23 12:12:42,325 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2021-09-23 12:43:38,826 - INFO: Pre-assembling mapped reads ...
2021-09-23 12:52:29,852 - INFO: Pre-assembling mapped reads finished.
2021-09-23 12:52:29,852 - INFO: Estimated embplant_pt-hitting base-coverage = 24913.72
2021-09-23 12:52:38,708 - INFO: Estimated word size(s): 71
2021-09-23 12:52:38,712 - INFO: Setting '-w 71'
2021-09-23 12:52:38,712 - INFO: Setting '--max-extending-len inf'
2021-09-23 12:53:59,663 - INFO: Checking seed reads and parameters finished.

2021-09-23 12:53:59,664 - INFO: Making read index ...
2021-09-23 14:12:01,793 - INFO: 401888432 candidates in all 541500654 reads
2021-09-23 14:12:05,570 - INFO: Pre-grouping reads ...
2021-09-23 14:12:05,570 - INFO: Setting '--pre-w 71'
2021-09-23 14:13:02,741 - INFO: 200000/48842976 used/duplicated
2021-09-23 14:13:15,225 - INFO: 7570 groups made.
2021-09-23 14:15:23,540 - INFO: Making read index finished.

2021-09-23 14:15:23,540 - INFO: Extending ...
2021-09-23 14:15:23,540 - INFO: Adding initial words ...
2021-09-23 14:27:27,248 - INFO: AW 42635598
2021-09-23 15:20:15,629 - INFO: Round 1: 401888432/401888432 AI 43163739 AW 98398754
2021-09-23 16:14:26,760 - INFO: Round 2: 401888432/401888432 AI 97683326 AW 178095002
2021-09-23 16:53:02,742 - INFO: Round 3: 401888432/401888432 AI 108918242 AW 198722238
2021-09-23 17:33:28,734 - INFO: Round 4: 401888432/401888432 AI 113980722 AW 209568790
2021-09-23 18:09:17,274 - INFO: Round 5: 401888432/401888432 AI 117524030 AW 216553860
2021-09-23 18:44:11,481 - INFO: Round 6: 401888432/401888432 AI 120614515 AW 221845384
2021-09-23 19:18:19,050 - INFO: Round 7: 401888432/401888432 AI 123202017 AW 226022484
2021-09-23 19:52:19,881 - INFO: Round 8: 401888432/401888432 AI 125298689 AW 229424104
2021-09-23 20:25:52,161 - INFO: Round 9: 401888432/401888432 AI 127113040 AW 232431310
2021-09-23 20:59:17,195 - INFO: Round 10: 401888432/401888432 AI 128789505 AW 235190308
2021-09-23 21:32:37,673 - INFO: Round 11: 401888432/401888432 AI 130320139 AW 237688624
2021-09-23 22:05:42,246 - INFO: Round 12: 401888432/401888432 AI 131695738 AW 239988832
2021-09-23 22:38:56,519 - INFO: Round 13: 401888432/401888432 AI 132989941 AW 242125502
2021-09-23 23:11:48,712 - INFO: Round 14: 401888432/401888432 AI 134197626 AW 244136476
2021-09-23 23:44:38,903 - INFO: Round 15: 401888432/401888432 AI 135329677 AW 245995638
2021-09-24 00:16:57,099 - INFO: Round 16: 401888432/401888432 AI 136352787 AW 247682474
2021-09-24 00:49:02,284 - INFO: Round 17: 401888432/401888432 AI 137289479 AW 249260546
2021-09-24 01:21:21,356 - INFO: Round 18: 401888432/401888432 AI 138162594 AW 250730112
2021-09-24 01:53:24,203 - INFO: Round 19: 401888432/401888432 AI 138980864 AW 252117582
2021-09-24 02:25:22,092 - INFO: Round 20: 401888432/401888432 AI 139758499 AW 253429916
2021-09-24 02:57:16,642 - INFO: Round 21: 401888432/401888432 AI 140513580 AW 254702776
2021-09-24 03:28:59,392 - INFO: Round 22: 401888432/401888432 AI 141236289 AW 255899338
2021-09-24 04:00:45,957 - INFO: Round 23: 401888432/401888432 AI 141902775 AW 257002688
2021-09-24 04:32:25,452 - INFO: Round 24: 401888432/401888432 AI 142500382 AW 258012938
2021-09-24 05:03:55,923 - INFO: Round 25: 401888432/401888432 AI 143064398 AW 258963274
2021-09-24 05:35:21,570 - INFO: Round 26: 401888432/401888432 AI 143589634 AW 259840866
2021-09-24 06:06:44,271 - INFO: Round 27: 401888432/401888432 AI 144072507 AW 260669916
2021-09-24 06:38:06,518 - INFO: Round 28: 401888432/401888432 AI 144527520 AW 261442210
2021-09-24 07:09:26,773 - INFO: Round 29: 401888432/401888432 AI 144964978 AW 262188850
2021-09-24 07:40:47,929 - INFO: Round 30: 401888432/401888432 AI 145376630 AW 262880166
2021-09-24 08:12:02,734 - INFO: Round 31: 401888432/401888432 AI 145753396 AW 263529542
2021-09-24 08:43:56,344 - INFO: Round 32: 401888432/401888432 AI 146119637 AW 264152584
2021-09-24 09:15:10,509 - INFO: Round 33: 401888432/401888432 AI 146457145 AW 264732822
2021-09-24 09:46:20,671 - INFO: Round 34: 401888432/401888432 AI 146777293 AW 265285272
2021-09-24 10:17:44,811 - INFO: Round 35: 401888432/401888432 AI 147080083 AW 265808908
2021-09-24 10:49:16,605 - INFO: Round 36: 401888432/401888432 AI 147374090 AW 266312276
2021-09-24 11:20:38,906 - INFO: Round 37: 401888432/401888432 AI 147653136 AW 266793344
2021-09-24 11:51:56,224 - INFO: Round 38: 401888432/401888432 AI 147915646 AW 267248066
2021-09-24 12:23:07,546 - INFO: Round 39: 401888432/401888432 AI 148178509 AW 267695246
2021-09-24 12:54:11,295 - INFO: Round 40: 401888432/401888432 AI 148421229 AW 268107660
2021-09-24 13:25:38,922 - INFO: Round 41: 401888432/401888432 AI 148643626 AW 268493934
2021-09-24 13:56:38,428 - INFO: Round 42: 401888432/401888432 AI 148859906 AW 268867166
2021-09-24 14:27:30,196 - INFO: Round 43: 401888432/401888432 AI 149073367 AW 269228476
2021-09-24 14:58:20,498 - INFO: Round 44: 401888432/401888432 AI 149273065 AW 269561168
2021-09-24 15:29:11,609 - INFO: Round 45: 401888432/401888432 AI 149452914 AW 269873504
2021-09-24 15:59:55,948 - INFO: Round 46: 401888432/401888432 AI 149628713 AW 270172762
2021-09-24 16:30:59,952 - INFO: Round 47: 401888432/401888432 AI 149794211 AW 270455328
2021-09-24 17:01:46,271 - INFO: Round 48: 401888432/401888432 AI 149947722 AW 270719696
2021-09-24 17:32:33,347 - INFO: Round 49: 401888432/401888432 AI 150085337 AW 270955308
2021-09-24 18:03:20,802 - INFO: Round 50: 401888432/401888432 AI 150215148 AW 271177334
2021-09-24 18:34:03,382 - INFO: Round 51: 401888432/401888432 AI 150340211 AW 271402862
2021-09-24 19:04:44,836 - INFO: Round 52: 401888432/401888432 AI 150475808 AW 271619304
2021-09-24 19:35:31,533 - INFO: Round 53: 401888432/401888432 AI 150592310 AW 271818624
2021-09-24 20:06:17,843 - INFO: Round 54: 401888432/401888432 AI 150704652 AW 272010134
2021-09-24 20:37:06,585 - INFO: Round 55: 401888432/401888432 AI 150814199 AW 272192900
2021-09-24 21:07:54,852 - INFO: Round 56: 401888432/401888432 AI 150919823 AW 272369190
2021-09-24 21:38:39,939 - INFO: Round 57: 401888432/401888432 AI 151020211 AW 272539784
2021-09-24 22:09:23,510 - INFO: Round 58: 401888432/401888432 AI 151117683 AW 272701990
2021-09-24 22:40:06,744 - INFO: Round 59: 401888432/401888432 AI 151206704 AW 272853854
2021-09-24 23:10:56,365 - INFO: Round 60: 401888432/401888432 AI 151290573 AW 272996102
2021-09-24 23:41:41,883 - INFO: Round 61: 401888432/401888432 AI 151370547 AW 273130244
2021-09-25 00:12:32,369 - INFO: Round 62: 401888432/401888432 AI 151443235 AW 273253142
2021-09-25 00:43:18,882 - INFO: Round 63: 401888432/401888432 AI 151511258 AW 273369700
2021-09-25 01:14:02,788 - INFO: Round 64: 401888432/401888432 AI 151578114 AW 273483222
2021-09-25 01:44:45,847 - INFO: Round 65: 401888432/401888432 AI 151638381 AW 273591272
2021-09-25 02:15:32,193 - INFO: Round 66: 401888432/401888432 AI 151696686 AW 273691072
2021-09-25 02:46:15,756 - INFO: Round 67: 401888432/401888432 AI 151752285 AW 273792338
2021-09-25 03:16:59,463 - INFO: Round 68: 401888432/401888432 AI 151812709 AW 273898984
2021-09-25 03:47:40,006 - INFO: Round 69: 401888432/401888432 AI 151873008 AW 273999134
2021-09-25 04:18:17,399 - INFO: Round 70: 401888432/401888432 AI 151929606 AW 274091324
2021-09-25 04:48:57,421 - INFO: Round 71: 401888432/401888432 AI 151978847 AW 274175700
2021-09-25 05:19:35,566 - INFO: Round 72: 401888432/401888432 AI 152024882 AW 274252320
2021-09-25 05:50:20,644 - INFO: Round 73: 401888432/401888432 AI 152065795 AW 274319234
2021-09-25 06:21:06,452 - INFO: Round 74: 401888432/401888432 AI 152105493 AW 274390016
2021-09-25 06:51:53,208 - INFO: Round 75: 401888432/401888432 AI 152147463 AW 274456434
2021-09-25 07:22:40,238 - INFO: Round 76: 401888432/401888432 AI 152184919 AW 274519544
2021-09-25 07:53:26,656 - INFO: Round 77: 401888432/401888432 AI 152220689 AW 274579026
2021-09-25 08:24:10,928 - INFO: Round 78: 401888432/401888432 AI 152254730 AW 274636348
2021-09-25 08:54:56,569 - INFO: Round 79: 401888432/401888432 AI 152288747 AW 274694686
2021-09-25 09:25:42,334 - INFO: Round 80: 401888432/401888432 AI 152322171 AW 274750568
2021-09-25 09:56:24,653 - INFO: Round 81: 401888432/401888432 AI 152354322 AW 274799278
2021-09-25 10:27:03,587 - INFO: Round 82: 401888432/401888432 AI 152381970 AW 274847944
2021-09-25 10:57:44,860 - INFO: Round 83: 401888432/401888432 AI 152411961 AW 274896230
2021-09-25 11:28:26,930 - INFO: Round 84: 401888432/401888432 AI 152441665 AW 274948690
2021-09-25 11:59:08,921 - INFO: Round 85: 401888432/401888432 AI 152477414 AW 275003816
2021-09-25 12:29:46,326 - INFO: Round 86: 401888432/401888432 AI 152504765 AW 275048644
2021-09-25 13:00:24,403 - INFO: Round 87: 401888432/401888432 AI 152529314 AW 275088556
2021-09-25 13:30:55,211 - INFO: Round 88: 401888432/401888432 AI 152550548 AW 275125268
2021-09-25 14:01:21,995 - INFO: Round 89: 401888432/401888432 AI 152568166 AW 275155216
2021-09-25 14:32:00,041 - INFO: Round 90: 401888432/401888432 AI 152586108 AW 275186946
2021-09-25 15:02:33,045 - INFO: Round 91: 401888432/401888432 AI 152604465 AW 275214266
2021-09-25 15:33:11,221 - INFO: Round 92: 401888432/401888432 AI 152620794 AW 275241006
2021-09-25 16:03:48,408 - INFO: Round 93: 401888432/401888432 AI 152635316 AW 275264294
2021-09-25 16:34:30,848 - INFO: Round 94: 401888432/401888432 AI 152650128 AW 275287058
2021-09-25 17:05:10,155 - INFO: Round 95: 401888432/401888432 AI 152665873 AW 275310712
2021-09-25 17:35:56,591 - INFO: Round 96: 401888432/401888432 AI 152679892 AW 275333764
2021-09-25 18:06:39,785 - INFO: Round 97: 401888432/401888432 AI 152697996 AW 275360310
2021-09-25 18:37:41,815 - INFO: Round 98: 401888432/401888432 AI 152713437 AW 275383004
2021-09-25 19:08:20,215 - INFO: Round 99: 401888432/401888432 AI 152725655 AW 275402024
2021-09-25 19:38:57,481 - INFO: Round 100: 401888432/401888432 AI 152735505 AW 275418048
2021-09-25 19:38:57,484 - INFO: Hit the round limit 100 and terminated ...
2021-09-25 20:05:20,826 - INFO: Extending finished.

2021-09-25 20:05:48,509 - INFO: Separating extended fastq file ... 
2021-09-25 20:18:42,271 - INFO: Setting '-k 21,33,45,65,85'
2021-09-25 20:18:42,271 - INFO: Assembling using SPAdes ...
2021-09-25 20:18:42,509 - INFO: spades.py -t 10  --phred-offset 33 -1 organelle6/extended_1_paired.fq -2 organelle6/extended_2_paired.fq --s1 organelle6/extended_1_unpaired.fq --s2 organelle6/extended_2_unpaired.fq -k 21,33,45,65,85 -o organelle6/extended_spades
2021-09-26 04:45:22,928 - INFO: Insert size = 255.147, deviation = 126.736, left quantile = 115, right quantile = 443
2021-09-26 04:45:22,929 - INFO: Assembling finished.

2021-09-26 05:59:55,094 - INFO: Slimming organelle6/extended_spades/K85/assembly_graph.fastg finished!
2021-09-26 07:38:40,945 - INFO: Slimming organelle6/extended_spades/K65/assembly_graph.fastg finished!
2021-09-26 12:12:56,417 - INFO: Slimming organelle6/extended_spades/K45/assembly_graph.fastg finished!
2021-09-26 12:12:56,417 - INFO: Slimming assembly graphs finished.

2021-09-26 12:12:56,418 - INFO: Extracting embplant_pt from the assemblies ...
2021-09-26 12:12:56,425 - INFO: Disentangling organelle6/extended_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 
2021-09-26 13:16:39,356 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_99421872_97620136_87808538_98497614_97618512_98129316_98216622_99260586_97717968_98528564_99260458_99260470_97725310_98237736_87950578_98212832_99260478_87806570_99260440_88541718_98216276_97222656_85837663_98711912_97934570_97934576_97095516_96272458_96272460_92228624_99260248!'
2021-09-26 13:16:40,449 - INFO: Disentangling organelle6/extended_spades/K65/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 
2021-09-26 14:36:40,246 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_123029288_122345818_122996982_123276123_118592988_106714069_120205569_122354881_122350663_123270886_123440831_123831997_123444663_9534854_123437961_122991110_123547163_122354927_123547165_122316393_123271844_123443313_123831911_118631180_120269037_120787565_122321959_123276141_120023534_122984603_122994212_122324952_123547529_120402229_106521408_120165538_122321209_122324620_123543899_123725873_123438971_122991356_122350755_123441999_123266390_123271192_122358239_123271194_122331632_120045147_123440451_120006510_123545041_118791934_120104543_123831659_120423071_120423065_120423069_123440805_122356035_120115083_123545147_122985621_123634284_123268120_122308835_123757699_123437945_122341615_123443417_123832185_123443419_122306445_123832183_122994138_123831761_123757705_123549712_123270012_122996998_123546953_123831759_108510338_120222245_122986167_122986165_122990300_108362072_117738974_120182271_123831995_120843073_123831923_108107250_123437799_123266546_123437801_120204327_123544257_108449768_123725626_120003708_120162738_123831707_123266734_117800778_123546531_122995990_120037577_123546045_123150232_123150244_120222853_116471540_122310835_112036992_123634670!'
2021-09-26 14:36:41,503 - INFO: Disentangling organelle6/extended_spades/K45/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 
2021-09-26 17:36:41,517 - INFO: Disentangling timeout. (see '--disentangle-time-limit' for more)
2021-09-26 17:36:44,424 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 
2021-09-26 17:36:44,425 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph.
2021-09-26 17:36:44,426 - INFO: Disentangling organelle6/extended_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 
2021-09-26 18:00:40,233 - WARNING: -100-bp gap/overlap between 87954368 and 88576826 indicated while conflicting connections existed!
2021-09-26 18:00:40,256 - WARNING: -100-bp gap/overlap between 85807831 and 85088573 indicated while conflicting connections existed!
2021-09-26 18:00:40,339 - WARNING: -100-bp gap/overlap between 84736430 and 82116214 indicated while conflicting connections existed!
2021-09-26 18:00:40,350 - WARNING: -100-bp gap/overlap between 85436025 and 82645207 indicated while conflicting connections existed!
2021-09-26 18:00:40,365 - WARNING: -100-bp gap/overlap between 88064606 and 85128207 indicated while conflicting connections existed!
2021-09-26 18:00:40,423 - WARNING: -100-bp gap/overlap between 84296229 and 89793572 indicated while conflicting connections existed!
2021-09-26 18:00:40,434 - WARNING: -100-bp gap/overlap between 96927608 and 96977658 indicated while conflicting connections existed!
2021-09-26 18:00:40,466 - WARNING: -100-bp gap/overlap between 85134827 and 91623884 indicated while conflicting connections existed!
2021-09-26 18:00:40,486 - WARNING: -100-bp gap/overlap between 99256306 and 87727905 indicated while conflicting connections existed!
2021-09-26 18:00:40,495 - WARNING: -100-bp gap/overlap between 85781931 and 85372403 indicated while conflicting connections existed!
2021-09-26 18:00:40,499 - WARNING: -100-bp gap/overlap between 85071582 and 84070320 indicated while conflicting connections existed!
2021-09-26 18:00:40,503 - WARNING: -100-bp gap/overlap between 93434352 and 80690724 indicated while conflicting connections existed!
2021-09-26 18:00:40,514 - WARNING: -100-bp gap/overlap between 85364815 and 85304287 indicated while conflicting connections existed!
2021-09-26 18:00:40,517 - WARNING: -100-bp gap/overlap between 85000053 and 84972971 indicated while conflicting connections existed!
2021-09-26 18:00:40,536 - WARNING: -100-bp overlap between 99129850 and 6932352 indicated while conflicting connections existed!
2021-09-26 18:00:40,544 - WARNING: -100-bp gap/overlap between 80340070 and 85839697 indicated while conflicting connections existed!
2021-09-26 18:00:40,550 - WARNING: -100-bp overlap between 97654134 and 11993180 indicated while conflicting connections existed!
2021-09-26 18:00:40,571 - WARNING: -100-bp overlap between 85117737 and 84938221 indicated while conflicting connections existed!
2021-09-26 18:00:41,237 - WARNING: Connection between 88403630_tail and 99260446_head already existed!
2021-09-26 18:00:41,238 - WARNING: Connection between 98497614_head and 97618512_head already existed!
2021-09-26 18:00:41,238 - WARNING: Connection between 84872604_head and 94792774_tail already existed!
2021-09-26 18:00:41,239 - WARNING: Connection between 84360013_head and 95674598_tail already existed!
2021-09-26 18:00:41,239 - WARNING: Connection between 97019784_tail and 89378338_head already existed!
2021-09-26 18:00:41,239 - WARNING: Connection between 80570620_head and 95379206_tail already existed!
2021-09-26 18:00:41,239 - WARNING: Connection between 82725218_head and 91450608_head already existed!
2021-09-26 18:56:18,521 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_99421872_97620136_87808538_98497614_97618512_98129316_98216622_99260586_97717968_98528564_99260458_99260470_97725310_98237736_87950578_98212832_99260478_87806570_99260440_88541718_98216276_97222656_85837663_98711912_97934570_97934576_97095516_96272458_96272460_92228624_99260248!'
2021-09-26 18:56:19,417 - INFO: Disentangling organelle6/extended_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a/an embplant_pt-insufficient graph ... 
2021-09-26 19:49:40,379 - INFO: Vertex_97621002_89419266_89419262_99260658_88276516_98165651_88289544_98721836_98721838_99390812_88715182_90357360_88172494_88379760_88293228_98528680_87966974_98546706_97773332_88482788_98710466_88492754_98216634_88281504_98216554_98894678_99390814_98894680_99035794_94385898_98511926_88403630_99260446_88233242_99260352_97719510_88148246_98212882_97719876_88220818_99260462_88101374_99260338_98216582_88564912_99260508_88243608_99260322_97727048_98527036_91015638_97621028_88717930 #copy = 2
2021-09-26 19:49:40,380 - INFO: Vertex_97677378_97725374_98206512_97725420_85026841_98528518_91415882_99260436 #copy = 1
2021-09-26 19:49:40,380 - INFO: Vertex_98212926_99260328_87951006_98942658_98216618_98528618_99260410_98216536_96996004_88073124_98513392_99250548 #copy = 1
2021-09-26 19:49:40,380 - INFO: Vertex_99421872_97620136_87808538_98497614_97618512_98129316_98216622_99260586_97717968_98528564_99260458_99260470_97725310_98237736_87950578_98212832_99260478_87806570_99260440_88541718_98216276_97222656_85837663_98711912_97934570_97934576_97095516_96272458_96272460_92228624_99260248 #copy = 1
2021-09-26 19:49:40,380 - INFO: Average embplant_pt kmer-coverage = 2418.5
2021-09-26 19:49:40,380 - INFO: Average embplant_pt base-coverage = 19484.8
2021-09-26 19:49:40,381 - INFO: Writing output ...
2021-09-26 19:49:40,506 - WARNING: More than one structure (gene order) produced ...
2021-09-26 19:49:40,506 - WARNING: Please check the final result to confirm whether they are simply different in SSC direction (two flip-flop configurations)!
2021-09-26 19:49:40,510 - INFO: Writing PATH1 of embplant_pt scaffold(s) to organelle6/embplant_pt.K85.scaffolds.graph1.1.path_sequence.fasta
2021-09-26 19:49:40,515 - INFO: Writing PATH2 of embplant_pt scaffold(s) to organelle6/embplant_pt.K85.scaffolds.graph1.2.path_sequence.fasta
2021-09-26 19:49:40,515 - INFO: Writing GRAPH to organelle6/embplant_pt.K85.contigs.graph1.selected_graph.gfa
2021-09-26 19:49:40,516 - INFO: Result status of embplant_pt: 1 scaffold(s)
2021-09-26 19:49:41,693 - INFO: Writing output finished.
2021-09-26 19:49:42,888 - INFO: Please ...
2021-09-26 19:49:42,888 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg' in K85,K65,K45
2021-09-26 19:49:42,888 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K85,K65,K45
2021-09-26 19:49:42,889 - INFO: visualize and confirm the incomplete result in Bandage.
2021-09-26 19:49:42,889 - INFO: If the result is nearly complete, 
2021-09-26 19:49:42,889 - INFO: you can also adjust the arguments according to https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#what-should-i-do-with-incomplete-resultbroken-assembly-graph
2021-09-26 19:49:42,889 - INFO: If you have questions for us, please provide us with the get_org.log.txt file and the post-slimming graph in the format you like!
2021-09-26 19:49:42,889 - INFO: Extracting embplant_pt from the assemblies finished.


Total cost 291583.72 s
Thank you!