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 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] PLATFORM: Linux MPLCLTLP0128 4.15.0-142-generic #146-Ubuntu SMP Tue Apr 13 01:11:19 UTC 2021 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.5; numpy 1.20.3; sympy 1.9; scipy 1.7.1; psutil 5.8.0 DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.9.0 GETORG_PATH=/home/2018jj001/.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/2018jj001/Assembly/GetOrganelle /home/2018jj001/anaconda3/bin/get_organelle_from_reads.py -1 Paired-Filter-Cutadapt-Demul-myr_R1-TAG-58.fastq -2 R2-Paired-Filter-Cutadapt-Demul-myr_R1-TAG-58.fastq -o SRR5602600-plastome -R 15 -F embplant_pt 2022-02-23 12:31:15,005 - INFO: Pre-reading fastq ... 2022-02-23 12:31:15,005 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf') 2022-02-23 12:31:15,144 - INFO: Tasting 100000+100000 reads ... 2022-02-23 12:31:28,148 - INFO: Tasting 500000+500000 reads ... 2022-02-23 12:32:15,950 - INFO: Tasting 2500000+2500000 reads ... 2022-02-23 12:35:48,159 - INFO: Estimating reads to use finished. 2022-02-23 12:37:24,341 - INFO: Counting read qualities ... 2022-02-23 12:37:24,840 - INFO: Identified quality encoding format = Illumina 1.8+ 2022-02-23 12:37:24,840 - INFO: Phred offset = 33 2022-02-23 12:37:24,841 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2022-02-23 12:37:24,919 - INFO: Mean error rate = 0.0016 2022-02-23 12:37:24,920 - INFO: Counting read lengths ... 2022-02-23 12:38:53,427 - INFO: Mean = 146.1 bp, maximum = 150 bp. 2022-02-23 12:38:53,427 - INFO: Reads used = 10164688+10164688 2022-02-23 12:38:53,427 - INFO: Pre-reading fastq finished. 2022-02-23 12:38:53,427 - INFO: Making seed reads ... 2022-02-23 12:38:53,475 - INFO: Seed bowtie2 index existed! 2022-02-23 12:38:53,476 - INFO: Mapping reads to seed bowtie2 index ... 2022-02-23 12:48:50,594 - INFO: Mapping finished. 2022-02-23 12:48:50,594 - INFO: Seed reads made: SRR5602600-plastome/seed/embplant_pt.initial.fq (15272668 bytes) 2022-02-23 12:48:50,594 - INFO: Making seed reads finished. 2022-02-23 12:48:50,594 - INFO: Checking seed reads and parameters ... 2022-02-23 12:48:50,595 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s). 2022-02-23 12:48:50,595 - INFO: If the result graph is not a circular organelle genome, 2022-02-23 12:48:50,595 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run. 2022-02-23 12:48:54,161 - INFO: Pre-assembling mapped reads ... 2022-02-23 12:49:17,875 - INFO: Pre-assembling mapped reads finished. 2022-02-23 12:49:17,875 - INFO: Estimated embplant_pt-hitting base-coverage = 69.40 2022-02-23 12:49:18,132 - INFO: Estimated word size(s): 95 2022-02-23 12:49:18,132 - INFO: Setting '-w 95' 2022-02-23 12:49:18,133 - INFO: Setting '--max-extending-len inf' 2022-02-23 12:49:18,259 - INFO: Checking seed reads and parameters finished. 2022-02-23 12:49:18,259 - INFO: Making read index ... 2022-02-23 12:53:27,757 - INFO: Mem 4.662 G, 18102640 candidates in all 20329376 reads 2022-02-23 12:53:27,827 - INFO: Pre-grouping reads ... 2022-02-23 12:53:27,827 - INFO: Setting '--pre-w 95' 2022-02-23 12:53:29,917 - INFO: Mem 4.199 G, 200000/1779067 used/duplicated 2022-02-23 12:53:52,720 - INFO: Mem 6.896 G, 7101 groups made. 2022-02-23 12:53:54,618 - INFO: Making read index finished. 2022-02-23 12:53:54,618 - INFO: Extending ... 2022-02-23 12:53:54,619 - INFO: Adding initial words ... 2022-02-23 12:53:56,606 - INFO: AW 686826 2022-02-23 12:56:35,082 - INFO: Round 1: 18102640/18102640 AI 50531 AW 850088 Mem 2.838 2022-02-23 12:59:11,644 - INFO: Round 2: 18102640/18102640 AI 61497 AW 945010 Mem 2.838 2022-02-23 13:01:47,425 - INFO: Round 3: 18102640/18102640 AI 70946 AW 1023022 Mem 2.838 2022-02-23 13:04:25,835 - INFO: Round 4: 18102640/18102640 AI 89556 AW 1186404 Mem 2.838 2022-02-23 13:07:02,603 - INFO: Round 5: 18102640/18102640 AI 114874 AW 1376310 Mem 2.838 2022-02-23 13:09:37,907 - INFO: Round 6: 18102640/18102640 AI 140340 AW 1565006 Mem 2.838 2022-02-23 13:12:13,191 - INFO: Round 7: 18102640/18102640 AI 164935 AW 1743104 Mem 2.838 2022-02-23 13:14:51,622 - INFO: Round 8: 18102640/18102640 AI 188837 AW 1914696 Mem 2.838 2022-02-23 13:17:29,395 - INFO: Round 9: 18102640/18102640 AI 210884 AW 2076360 Mem 2.838 2022-02-23 13:20:09,513 - INFO: Round 10: 18102640/18102640 AI 232913 AW 2240936 Mem 2.838 2022-02-23 13:22:50,238 - INFO: Round 11: 18102640/18102640 AI 254509 AW 2403234 Mem 2.838 2022-02-23 13:25:30,758 - INFO: Round 12: 18102640/18102640 AI 276796 AW 2566212 Mem 2.962 2022-02-23 13:28:05,865 - INFO: Round 13: 18102640/18102640 AI 297351 AW 2712692 Mem 2.962 2022-02-23 13:30:41,145 - INFO: Round 14: 18102640/18102640 AI 316065 AW 2847344 Mem 2.962 2022-02-23 13:33:16,614 - INFO: Round 15: 18102640/18102640 AI 333910 AW 2980852 Mem 2.962 2022-02-23 13:33:16,614 - INFO: Hit the round limit 15 and terminated ... 2022-02-23 13:34:28,207 - INFO: Extending finished. 2022-02-23 13:34:28,735 - INFO: Separating extended fastq file ... 2022-02-23 13:34:30,722 - INFO: Setting '-k 21,55,85,115' 2022-02-23 13:34:30,723 - INFO: Assembling using SPAdes ... 2022-02-23 13:34:31,204 - WARNING: Compression after read correction will be skipped for lack of 'pigz' 2022-02-23 13:34:31,205 - INFO: /home/2018jj001/anaconda3/lib/python3.9/site-packages/GetOrganelleDep/linux/SPAdes/bin/spades.py -t 1 --disable-gzip-output --phred-offset 33 -1 SRR5602600-plastome/extended_1_paired.fq -2 SRR5602600-plastome/extended_2_paired.fq --s1 SRR5602600-plastome/extended_1_unpaired.fq --s2 SRR5602600-plastome/extended_2_unpaired.fq -k 21,55,85,115 -o SRR5602600-plastome/extended_spades 2022-02-23 13:38:59,431 - INFO: Insert size = 272.726, deviation = 82.4494, left quantile = 182, right quantile = 382 2022-02-23 13:38:59,432 - INFO: Assembling finished. 2022-02-23 13:39:03,199 - INFO: Slimming SRR5602600-plastome/extended_spades/K115/assembly_graph.fastg finished! 2022-02-23 13:39:05,030 - INFO: Slimming SRR5602600-plastome/extended_spades/K85/assembly_graph.fastg finished! 2022-02-23 13:39:06,857 - INFO: Slimming SRR5602600-plastome/extended_spades/K55/assembly_graph.fastg finished! 2022-02-23 13:39:06,858 - INFO: Slimming assembly graphs finished. 2022-02-23 13:39:06,858 - INFO: Extracting embplant_pt from the assemblies ... 2022-02-23 13:39:06,859 - INFO: Disentangling SRR5602600-plastome/extended_spades/K115/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2022-02-23 13:39:07,178 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2022-02-23 13:39:07,179 - INFO: Disentangling SRR5602600-plastome/extended_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2022-02-23 13:39:07,742 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?' 2022-02-23 13:39:07,742 - INFO: Disentangling SRR5602600-plastome/extended_spades/K55/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2022-02-23 13:39:09,342 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_206088!' 2022-02-23 13:39:09,343 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 2022-02-23 13:39:09,343 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph. 2022-02-23 13:39:09,343 - INFO: Disentangling SRR5602600-plastome/extended_spades/K115/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 2022-02-23 13:39:09,390 - INFO: Disentangling failed: 'No new connections.' 2022-02-23 13:39:09,391 - INFO: Disentangling SRR5602600-plastome/extended_spades/K115/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a/an embplant_pt-insufficient graph ... 2022-02-23 13:39:11,029 - WARNING: The graph might suffer from contamination or polymorphism! 2022-02-23 13:39:11,029 - WARNING: Only the contig with the max cov was kept for each of those 2 polymorphic loci. 2022-02-23 14:00:19,251 - INFO: Vertex_179044 #copy = 2 2022-02-23 14:00:19,251 - INFO: Vertex_186162 #copy = 1 2022-02-23 14:00:19,251 - INFO: Vertex_186184 #copy = 1 2022-02-23 14:00:19,251 - INFO: Vertex_186218 #copy = 1 2022-02-23 14:00:19,251 - INFO: Vertex_186226 #copy = 1 2022-02-23 14:00:19,251 - INFO: Vertex_186238_169358_32058_168538_185452_6974_186202 #copy = 1 2022-02-23 14:00:19,251 - INFO: Vertex_186240_186082_22814_185808_185406_43484_186270 #copy = 1 2022-02-23 14:00:19,252 - INFO: Vertex_186246_186330_186084 #copy = 2 2022-02-23 14:00:19,252 - INFO: Average embplant_pt kmer-coverage = 12.0 2022-02-23 14:00:19,252 - INFO: Average embplant_pt base-coverage = 54.5 2022-02-23 14:00:19,252 - INFO: Writing output ... 2022-02-23 14:00:19,355 - WARNING: Multiple structures (gene order) produced! 2022-02-23 14:00:19,355 - WARNING: Please check the existence of those isomers by using reads mapping (library information) or longer reads. 2022-02-23 14:00:19,358 - INFO: Writing PATH1 of embplant_pt scaffold(s) to SRR5602600-plastome/embplant_pt.K115.scaffolds.graph1.1.path_sequence.fasta 2022-02-23 14:00:19,361 - INFO: Writing PATH2 of embplant_pt scaffold(s) to SRR5602600-plastome/embplant_pt.K115.scaffolds.graph1.2.path_sequence.fasta 2022-02-23 14:00:19,363 - INFO: Writing PATH3 of embplant_pt scaffold(s) to SRR5602600-plastome/embplant_pt.K115.scaffolds.graph1.3.path_sequence.fasta 2022-02-23 14:00:19,367 - INFO: Writing PATH4 of embplant_pt scaffold(s) to SRR5602600-plastome/embplant_pt.K115.scaffolds.graph1.4.path_sequence.fasta 2022-02-23 14:00:19,367 - INFO: Writing GRAPH to SRR5602600-plastome/embplant_pt.K115.contigs.graph1.selected_graph.gfa 2022-02-23 14:00:19,368 - INFO: Result status of embplant_pt: 3 scaffold(s) 2022-02-23 14:00:19,644 - INFO: Writing output finished. 2022-02-23 14:00:19,647 - INFO: Please ... 2022-02-23 14:00:19,648 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg' in K115,K85,K55 2022-02-23 14:00:19,648 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K115,K85,K55 2022-02-23 14:00:19,648 - INFO: visualize and confirm the incomplete result in Bandage. 2022-02-23 14:00:19,648 - INFO: If the result is nearly complete, 2022-02-23 14:00:19,648 - 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 2022-02-23 14:00:19,648 - 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! 2022-02-23 14:00:19,649 - INFO: Extracting embplant_pt from the assemblies finished. Total cost 5346.48 s Thank you!