GetOrganelle v1.7.7.0 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 3.7.16 (default, Jan 17 2023, 22:20:44) [GCC 11.2.0] PLATFORM: Linux localhost.localdomain 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.21.6; sympy 1.10.1; scipy 1.7.3 DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.5.0 GETORG_PATH=/home/.GetOrganelle SEED DB: embplant_pt 0.0.1; embplant_mt 0.0.1 LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1 WORKING DIR: /home/workspace/plasmid/cp /home/program/miniconda3/envs/getorganelle/bin/get_organelle_from_reads.py -1 seq/PYA1/PYA1_clean_R1.fastq.gz -2 seq/PYA1/PYA1_clean_R2.fastq.gz -o temp/round50_k12_seedetc/PYA1_new -t 24 -F embplant_pt -R 50 -k 21,29,39,45,59,65,79,85,99,105,119,141 -w 85 --max-reads inf --reduce-reads-for-coverage inf --continue 2024-01-16 16:48:53,489 - INFO: Pre-reading fastq ... 2024-01-16 16:48:53,489 - INFO: Unzipping reads file: seq/PYA1/PYA1_clean_R1.fastq.gz (336138874 bytes) 2024-01-16 16:49:08,616 - INFO: Unzipping reads file: seq/PYA1/PYA1_clean_R2.fastq.gz (353010314 bytes) 2024-01-16 16:49:24,379 - INFO: Counting read qualities ... 2024-01-16 16:49:24,733 - INFO: Identified quality encoding format = Sanger 2024-01-16 16:49:24,733 - INFO: Phred offset = 33 2024-01-16 16:49:24,737 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2024-01-16 16:49:24,813 - INFO: Mean error rate = 0.0019 2024-01-16 16:49:24,815 - INFO: Counting read lengths ... 2024-01-16 16:49:54,898 - INFO: Mean = 146.8 bp, maximum = 150 bp. 2024-01-16 16:49:54,898 - INFO: Reads used = 4926631+4926631 2024-01-16 16:49:54,898 - INFO: Pre-reading fastq finished. 2024-01-16 16:49:54,898 - INFO: Making seed reads ... 2024-01-16 16:49:54,900 - INFO: Seed bowtie2 index existed! 2024-01-16 16:49:54,900 - INFO: Mapping reads to seed bowtie2 index ... 2024-01-16 16:59:25,830 - INFO: Mapping finished. 2024-01-16 16:59:25,830 - INFO: Seed reads made: temp/round50_k12_seedetc/PYA1_new/seed/embplant_pt.initial.fq (208515530 bytes) 2024-01-16 16:59:25,832 - INFO: Making seed reads finished. 2024-01-16 16:59:25,832 - INFO: Checking seed reads and parameters ... 2024-01-16 17:00:24,045 - INFO: Estimated embplant_pt-hitting base-coverage = 384.06 2024-01-16 17:00:24,702 - INFO: Setting '--max-extending-len inf' 2024-01-16 17:00:27,061 - INFO: Checking seed reads and parameters finished. 2024-01-16 17:00:27,061 - INFO: Making read index ... 2024-01-16 17:03:04,942 - INFO: 7480407 candidates in all 9853262 reads 2024-01-16 17:03:04,943 - INFO: Pre-grouping reads ... 2024-01-16 17:03:04,943 - INFO: Setting '--pre-w 85' 2024-01-16 17:03:07,449 - INFO: 200000/1599666 used/duplicated 2024-01-16 17:03:56,574 - INFO: 1728 groups made. 2024-01-16 17:04:01,784 - INFO: Making read index finished. 2024-01-16 17:04:01,785 - INFO: Extending ... 2024-01-16 17:04:01,785 - INFO: Adding initial words ... 2024-01-16 17:04:55,363 - INFO: AW 5012768 2024-01-16 17:07:10,070 - INFO: Round 1: 7480407/7480407 AI 217746 AW 5478798 2024-01-16 17:09:13,653 - INFO: Round 2: 7480407/7480407 AI 258885 AW 7171188 2024-01-16 17:11:26,164 - INFO: Round 3: 7480407/7480407 AI 433906 AW 14073744 2024-01-16 17:13:32,677 - INFO: Round 4: 7480407/7480407 AI 526670 AW 17211916 2024-01-16 17:15:36,433 - INFO: Round 5: 7480407/7480407 AI 590021 AW 18890404 2024-01-16 17:17:37,801 - INFO: Round 6: 7480407/7480407 AI 611234 AW 19489204 2024-01-16 17:19:37,769 - INFO: Round 7: 7480407/7480407 AI 616325 AW 19656902 2024-01-16 17:21:39,211 - INFO: Round 8: 7480407/7480407 AI 618843 AW 19752748 2024-01-16 17:23:38,795 - INFO: Round 9: 7480407/7480407 AI 622843 AW 19910058 2024-01-16 17:25:37,306 - INFO: Round 10: 7480407/7480407 AI 627731 AW 20109596 2024-01-16 17:27:36,527 - INFO: Round 11: 7480407/7480407 AI 632073 AW 20276550 2024-01-16 17:29:32,641 - INFO: Round 12: 7480407/7480407 AI 634855 AW 20378378 2024-01-16 17:31:27,108 - INFO: Round 13: 7480407/7480407 AI 635728 AW 20411730 2024-01-16 17:33:23,557 - INFO: Round 14: 7480407/7480407 AI 636294 AW 20432034 2024-01-16 17:35:23,401 - INFO: Round 15: 7480407/7480407 AI 636753 AW 20446296 2024-01-16 17:37:26,364 - INFO: Round 16: 7480407/7480407 AI 637211 AW 20461314 2024-01-16 17:39:36,543 - INFO: Round 17: 7480407/7480407 AI 637602 AW 20473880 2024-01-16 17:41:36,982 - INFO: Round 18: 7480407/7480407 AI 638007 AW 20486668 2024-01-16 17:43:37,716 - INFO: Round 19: 7480407/7480407 AI 638244 AW 20495392 2024-01-16 17:45:38,195 - INFO: Round 20: 7480407/7480407 AI 638563 AW 20505528 2024-01-16 17:47:38,445 - INFO: Round 21: 7480407/7480407 AI 638754 AW 20511390 2024-01-16 17:49:39,632 - INFO: Round 22: 7480407/7480407 AI 638941 AW 20517156 2024-01-16 17:51:44,153 - INFO: Round 23: 7480407/7480407 AI 639156 AW 20523144 2024-01-16 17:53:42,825 - INFO: Round 24: 7480407/7480407 AI 639353 AW 20528294 2024-01-16 17:55:36,876 - INFO: Round 25: 7480407/7480407 AI 639553 AW 20534286 2024-01-16 17:57:22,291 - INFO: Round 26: 7480407/7480407 AI 639695 AW 20538238 2024-01-16 17:59:09,135 - INFO: Round 27: 7480407/7480407 AI 639832 AW 20542124 2024-01-16 18:00:58,860 - INFO: Round 28: 7480407/7480407 AI 639947 AW 20545544 2024-01-16 18:02:49,643 - INFO: Round 29: 7480407/7480407 AI 640187 AW 20551958 2024-01-16 18:04:41,893 - INFO: Round 30: 7480407/7480407 AI 640405 AW 20557376 2024-01-16 18:06:40,554 - INFO: Round 31: 7480407/7480407 AI 640573 AW 20561614 2024-01-16 18:09:48,115 - INFO: Round 32: 7480407/7480407 AI 640711 AW 20565154 2024-01-16 18:12:37,432 - INFO: Round 33: 7480407/7480407 AI 640828 AW 20568650 2024-01-16 18:14:53,687 - INFO: Round 34: 7480407/7480407 AI 640935 AW 20571878 2024-01-16 18:17:05,857 - INFO: Round 35: 7480407/7480407 AI 641090 AW 20575468 2024-01-16 18:19:11,073 - INFO: Round 36: 7480407/7480407 AI 641183 AW 20578040 2024-01-16 18:21:19,572 - INFO: Round 37: 7480407/7480407 AI 641265 AW 20580154 2024-01-16 18:23:31,116 - INFO: Round 38: 7480407/7480407 AI 641409 AW 20584786 2024-01-16 18:25:42,563 - INFO: Round 39: 7480407/7480407 AI 641581 AW 20589580 2024-01-16 18:28:09,297 - INFO: Round 40: 7480407/7480407 AI 641738 AW 20593622 2024-01-16 18:30:15,846 - INFO: Round 41: 7480407/7480407 AI 641882 AW 20597710 2024-01-16 18:32:45,842 - INFO: Round 42: 7480407/7480407 AI 642021 AW 20600730 2024-01-16 18:34:40,283 - INFO: Round 43: 7480407/7480407 AI 642126 AW 20603412 2024-01-16 18:36:38,112 - INFO: Round 44: 7480407/7480407 AI 642232 AW 20606498 2024-01-16 18:38:33,512 - INFO: Round 45: 7480407/7480407 AI 642343 AW 20609280 2024-01-16 18:40:31,584 - INFO: Round 46: 7480407/7480407 AI 642491 AW 20613632 2024-01-16 18:42:42,060 - INFO: Round 47: 7480407/7480407 AI 642627 AW 20617544 2024-01-16 18:44:34,799 - INFO: Round 48: 7480407/7480407 AI 642798 AW 20621740 2024-01-16 18:46:28,602 - INFO: Round 49: 7480407/7480407 AI 642928 AW 20625196 2024-01-16 18:48:21,703 - INFO: Round 50: 7480407/7480407 AI 643025 AW 20627530 2024-01-16 18:48:21,703 - INFO: Hit the round limit 50 and terminated ... 2024-01-16 18:49:15,199 - INFO: Extending finished. 2024-01-16 18:49:16,178 - INFO: Separating extended fastq file ... 2024-01-16 18:49:24,666 - INFO: Setting '-k 21,29,39,45,59,65,79,85,99,105,119' 2024-01-16 18:49:24,667 - INFO: Assembling using SPAdes ... 2024-01-16 18:49:24,768 - INFO: spades.py -t 24 --phred-offset 33 -1 temp/round50_k12_seedetc/PYA1_new/extended_1_paired.fq -2 temp/round50_k12_seedetc/PYA1_new/extended_2_paired.fq --s1 temp/round50_k12_seedetc/PYA1_new/extended_1_unpaired.fq --s2 temp/round50_k12_seedetc/PYA1_new/extended_2_unpaired.fq -k 21,29,39,45,59,65,79,85,99,105,119 -o temp/round50_k12_seedetc/PYA1_new/extended_spades 2024-01-16 19:17:28,330 - INFO: Insert size = 232.018, deviation = 55.1599, left quantile = 163, right quantile = 305 2024-01-16 19:17:28,331 - INFO: Assembling finished. 2024-01-16 19:17:32,957 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K119/assembly_graph.fastg finished! 2024-01-16 19:17:36,985 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K105/assembly_graph.fastg finished! 2024-01-16 19:17:41,341 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K99/assembly_graph.fastg finished! 2024-01-16 19:17:45,947 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K85/assembly_graph.fastg finished! 2024-01-16 19:17:50,629 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K79/assembly_graph.fastg finished! 2024-01-16 19:17:59,140 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K65/assembly_graph.fastg finished! 2024-01-16 19:18:05,582 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K59/assembly_graph.fastg finished! 2024-01-16 19:18:19,645 - INFO: Slimming temp/round50_k12_seedetc/PYA1_new/extended_spades/K45/assembly_graph.fastg finished! 2024-01-16 19:18:19,645 - INFO: Slimming assembly graphs finished. 2024-01-16 19:18:19,646 - INFO: Extracting embplant_pt from the assemblies ... 2024-01-16 19:18:20,078 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K119/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:20,400 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:20,401 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:20,576 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:20,576 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K99/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:20,851 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:20,852 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:21,025 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:21,026 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K79/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:21,247 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:21,247 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K65/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:22,121 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:22,122 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K59/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:22,353 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:22,354 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K45/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:23,782 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2024-01-16 19:18:23,783 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 2024-01-16 19:18:23,783 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph. 2024-01-16 19:18:23,783 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K119/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-01-16 19:18:23,908 - WARNING: -200-bp gap/overlap between 356064 and 2771392 indicated while conflicting connections existed! 2024-01-16 19:18:23,948 - WARNING: -200-bp gap/overlap between 2772750 and 2772704 indicated while conflicting connections existed! 2024-01-16 19:18:23,966 - WARNING: -500-bp gap/overlap between 2773662 and 2772820 indicated while conflicting connections existed! 2024-01-16 19:18:23,976 - WARNING: -500-bp gap/overlap between 2772270 and 2772796 indicated while conflicting connections existed! 2024-01-16 19:18:23,982 - WARNING: -500-bp gap/overlap between 2773474 and 2771584 indicated while conflicting connections existed! 2024-01-16 19:18:24,019 - WARNING: -500-bp gap/overlap between 2772168 and 2772776 indicated while conflicting connections existed! 2024-01-16 19:18:24,029 - WARNING: -500-bp gap/overlap between 2772170 and 2685632 indicated while conflicting connections existed! 2024-01-16 19:18:24,038 - INFO: Disentangling failed: 'No new connections.' 2024-01-16 19:18:24,039 - INFO: Disentangling temp/round50_k12_seedetc/PYA1_new/extended_spades/K119/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a/an embplant_pt-insufficient graph ... 2024-01-16 19:18:24,761 - INFO: Average embplant_pt kmer-coverage = 137.0 2024-01-16 19:18:24,761 - INFO: Average embplant_pt base-coverage = 698.4 2024-01-16 19:18:24,761 - INFO: Writing output ... 2024-01-16 19:18:24,917 - INFO: Writing PATH1 of embplant_pt scaffold(s) to temp/round50_k12_seedetc/PYA1_new/embplant_pt.K119.scaffolds.graph1.1.path_sequence.fasta 2024-01-16 19:18:24,918 - INFO: Writing GRAPH to temp/round50_k12_seedetc/PYA1_new/embplant_pt.K119.contigs.graph1.selected_graph.gfa 2024-01-16 19:18:24,919 - INFO: Result status of embplant_pt: 6 scaffold(s) 2024-01-16 19:18:25,280 - INFO: Writing output finished. 2024-01-16 19:18:25,281 - INFO: Please ... 2024-01-16 19:18:25,281 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg' in K119,K105,K99,K85,K79,K65,K59,K45 2024-01-16 19:18:25,281 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K119,K105,K99,K85,K79,K65,K59,K45 2024-01-16 19:18:25,281 - INFO: visualize and confirm the incomplete result in Bandage. 2024-01-16 19:18:25,281 - INFO: If the result is nearly complete, 2024-01-16 19:18:25,282 - 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 2024-01-16 19:18:25,282 - 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! 2024-01-16 19:18:25,282 - INFO: Extracting embplant_pt from the assemblies finished. Total cost 8973.95 s Thank you!