GetOrganelle v1.7.7.1 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 3.8.19 (default, Mar 20 2024, 19:58:24) [GCC 11.2.0] PLATFORM: Linux yyzw-System-Product-Name 6.8.0-39-generic #39-Ubuntu SMP PREEMPT_DYNAMIC Fri Jul 5 21:49:14 UTC 2024 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.7.1; numpy 1.24.3; sympy 1.12; scipy 1.10.1 DEPENDENCIES: Bowtie2 2.4.1; SPAdes 3.13.1; Blast 2.5.0 GETORG_PATH=/home/yyzw/.GetOrganelle LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1 WORKING_DIR=/home/yyzw /home/yyzw/miniconda3/envs/chloroplast/bin/get_organelle_from_reads.py -1 /home/yyzw/chm/data1/07_1.fq.gz -2 /home/yyzw/chm/data1/07_2.fq.gz -o /home/yyzw/chm/data2/07_3 -w 88 -R 15 -k 21,45,65,85,105 --reduce-reads-for-coverage=1000 -t 12 -F embplant_pt -s /home/yyzw/chm/data1/fasta/2429_11_2_crenata.fasta 2024-08-03 17:38:01,509 - INFO: Pre-reading fastq ... 2024-08-03 17:38:01,509 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf') 2024-08-03 17:38:01,551 - INFO: Tasting 100000+100000 reads ... 2024-08-03 17:38:03,593 - INFO: Tasting 500000+500000 reads ... 2024-08-03 17:38:08,888 - INFO: Estimating reads to use finished. 2024-08-03 17:38:08,889 - INFO: Unzipping reads file: /home/yyzw/chm/data1/07_1.fq.gz (733483441 bytes) 2024-08-03 17:38:20,583 - INFO: Unzipping reads file: /home/yyzw/chm/data1/07_2.fq.gz (730148790 bytes) 2024-08-03 17:38:32,256 - INFO: Counting read qualities ... 2024-08-03 17:38:32,304 - INFO: Identified quality encoding format = Sanger 2024-08-03 17:38:32,304 - INFO: Phred offset = 33 2024-08-03 17:38:32,305 - INFO: Trimming bases with qualities (0.05%): 33..33 ! 2024-08-03 17:38:32,318 - INFO: Mean error rate = 0.0019 2024-08-03 17:38:32,319 - INFO: Counting read lengths ... 2024-08-03 17:38:41,238 - INFO: Mean = 150.0 bp, maximum = 150 bp. 2024-08-03 17:38:41,238 - INFO: Reads used = 12149525+12149525 2024-08-03 17:38:41,238 - INFO: Pre-reading fastq finished. 2024-08-03 17:38:41,238 - INFO: Making seed reads ... 2024-08-03 17:38:41,240 - INFO: Making seed - bowtie2 index ... 2024-08-03 17:38:41,379 - INFO: Making seed - bowtie2 index finished. 2024-08-03 17:38:41,379 - INFO: Mapping reads to seed bowtie2 index ... 2024-08-03 17:39:47,258 - INFO: Mapping finished. 2024-08-03 17:39:47,258 - INFO: Seed reads made: /home/yyzw/chm/data2/07_3/seed/embplant_pt.initial.fq (63738528 bytes) 2024-08-03 17:39:47,258 - INFO: Making seed reads finished. 2024-08-03 17:39:47,259 - INFO: Checking seed reads and parameters ... 2024-08-03 17:39:50,673 - INFO: Estimated embplant_pt-hitting base-coverage = 281.48 2024-08-03 17:39:50,782 - INFO: Setting '--max-extending-len inf' 2024-08-03 17:39:50,878 - INFO: Checking seed reads and parameters finished. 2024-08-03 17:39:50,878 - INFO: Making read index ... 2024-08-03 17:40:52,329 - INFO: 22877153 candidates in all 24299050 reads 2024-08-03 17:40:52,329 - INFO: Pre-grouping reads ... 2024-08-03 17:40:52,329 - INFO: Setting '--pre-w 88' 2024-08-03 17:40:52,926 - INFO: 200000/686360 used/duplicated 2024-08-03 17:41:01,570 - INFO: 3581 groups made. 2024-08-03 17:41:02,362 - INFO: Making read index finished. 2024-08-03 17:41:02,362 - INFO: Extending ... 2024-08-03 17:41:02,362 - INFO: Adding initial words ... 2024-08-03 17:41:05,878 - INFO: AW 2219082 2024-08-03 17:43:04,012 - INFO: Round 1: 22877153/22877153 AI 655550 AW 12518648 2024-08-03 17:45:09,293 - INFO: Round 2: 22877153/22877153 AI 2765020 AW 47657146 2024-08-03 17:46:53,240 - INFO: Round 3: 22877153/22877153 AI 3914887 AW 70661492 2024-08-03 17:48:32,450 - INFO: Round 4: 22877153/22877153 AI 4456387 AW 84109995 2024-08-03 17:50:05,794 - INFO: Round 5: 22877153/22877153 AI 4792686 AW 92879941 2024-08-03 17:51:36,891 - INFO: Round 6: 22877153/22877153 AI 4992962 AW 98602485 2024-08-03 17:53:04,198 - INFO: Round 7: 22877153/22877153 AI 5132085 AW 102700529 2024-08-03 17:54:31,163 - INFO: Round 8: 22877153/22877153 AI 5228366 AW 105724945 2024-08-03 17:55:56,138 - INFO: Round 9: 22877153/22877153 AI 5300998 AW 107992140 2024-08-03 17:57:20,839 - INFO: Round 10: 22877153/22877153 AI 5358755 AW 109752074 2024-08-03 17:58:45,309 - INFO: Round 11: 22877153/22877153 AI 5403963 AW 111090644 2024-08-03 18:00:09,566 - INFO: Round 12: 22877153/22877153 AI 5436220 AW 112095922 2024-08-03 18:01:33,756 - INFO: Round 13: 22877153/22877153 AI 5463948 AW 112944510 2024-08-03 18:02:57,753 - INFO: Round 14: 22877153/22877153 AI 5487488 AW 113659284 2024-08-03 18:04:21,695 - INFO: Round 15: 22877153/22877153 AI 5504969 AW 114199522 2024-08-03 18:04:21,695 - INFO: Hit the round limit 15 and terminated ... 2024-08-03 18:04:43,343 - INFO: Extending finished. 2024-08-03 18:04:43,816 - INFO: Separating extended fastq file ... 2024-08-03 18:04:49,854 - INFO: Setting '-k 21,45,65,85,105' 2024-08-03 18:04:49,854 - INFO: Assembling using SPAdes ... 2024-08-03 18:04:49,870 - INFO: spades.py -t 12 --phred-offset 33 -1 /home/yyzw/chm/data2/07_3/extended_1_paired.fq -2 /home/yyzw/chm/data2/07_3/extended_2_paired.fq --s1 /home/yyzw/chm/data2/07_3/extended_1_unpaired.fq --s2 /home/yyzw/chm/data2/07_3/extended_2_unpaired.fq -k 21,45,65,85,105 -o /home/yyzw/chm/data2/07_3/extended_spades 2024-08-03 18:26:54,510 - INFO: Insert size = 212.779, deviation = 58.8188, left quantile = 154, right quantile = 294 2024-08-03 18:26:54,510 - INFO: Assembling finished. 2024-08-03 18:27:08,448 - INFO: Slimming /home/yyzw/chm/data2/07_3/extended_spades/K105/assembly_graph.fastg finished! 2024-08-03 18:27:08,448 - INFO: Slimming assembly graphs finished. 2024-08-03 18:27:08,448 - INFO: Extracting embplant_pt from the assemblies ... 2024-08-03 18:27:08,448 - INFO: Disentangling /home/yyzw/chm/data2/07_3/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-08-03 18:27:08,748 - INFO: Disentangling unsuccessful: 'Incomplete/Complicated graph: please check around EDGE_16415938_17069458_17253306!' 2024-08-03 18:27:08,748 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 2024-08-03 18:27:08,748 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph. 2024-08-03 18:27:08,748 - INFO: Disentangling /home/yyzw/chm/data2/07_3/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2024-08-03 18:27:09,167 - INFO: Disentangling unsuccessful: 'Incomplete/Complicated graph: please check around EDGE_16415938_17069458_17253306!' 2024-08-03 18:27:09,167 - INFO: Disentangling /home/yyzw/chm/data2/07_3/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a/an embplant_pt-insufficient graph ... 2024-08-03 18:27:09,776 - INFO: Average embplant_pt kmer-coverage = 63.5 2024-08-03 18:27:09,776 - INFO: Average embplant_pt base-coverage = 207.1 2024-08-03 18:27:09,776 - INFO: Writing output ... 2024-08-03 18:27:09,796 - INFO: Writing PATH1 of embplant_pt scaffold(s) to /home/yyzw/chm/data2/07_3/embplant_pt.K105.scaffolds.graph1.1.path_sequence.fasta 2024-08-03 18:27:09,796 - INFO: Writing GRAPH to /home/yyzw/chm/data2/07_3/embplant_pt.K105.contigs.graph1.selected_graph.gfa 2024-08-03 18:27:09,796 - INFO: Result status of embplant_pt: 8 scaffold(s) 2024-08-03 18:27:09,815 - INFO: Writing output finished. 2024-08-03 18:27:09,815 - INFO: Please ... 2024-08-03 18:27:09,815 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg' in K105 2024-08-03 18:27:09,815 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K105 2024-08-03 18:27:09,815 - INFO: visualize and confirm the incomplete result in Bandage. 2024-08-03 18:27:09,815 - INFO: If the result is nearly complete, 2024-08-03 18:27:09,815 - 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 2024-08-03 18:27:09,815 - 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! 2024-08-03 18:27:09,815 - INFO: Extracting embplant_pt from the assemblies finished. Total cost 2948.82 s Thank you!