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 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0] PLATFORM: Linux mike115 4.18.0-477.27.1.el8_8.x86_64 #1 SMP Thu Aug 31 10:29:22 EDT 2023 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.7.1; numpy 2.1.3; sympy 1.13.3; scipy 1.14.1 DEPENDENCIES: Bowtie2 2.5.4; SPAdes 4.0.0; Blast 2.16.0 GETORG_PATH=/home/mvanda3/.GetOrganelle SEED DB: embplant_pt 0.0.1; embplant_mt 0.0.1 WORKING_DIR=/ddnA/project/smathews/mvanda3/Amyema_genomes/00_fastq/23-275 /work/mvanda3/.conda/envs/BIOSET/bin/get_organelle_from_reads.py -1 23-275_unclassified_1.fastq -2 23-275_unclassified_2.fastq -w 101 -o 23-275_enriched_plastome_assembly_unclassified2 -F embplant_pt --genes Loranth_refdata.fasta -R 200 -k 21,55,85,115 --reduce-reads-for-coverage inf --max-reads 20000000 2025-02-06 10:04:30,880 - INFO: Pre-reading fastq ... 2025-02-06 10:04:50,057 - INFO: Counting read qualities ... 2025-02-06 10:04:50,148 - INFO: Identified quality encoding format = Sanger 2025-02-06 10:04:50,148 - INFO: Phred offset = 33 2025-02-06 10:04:50,148 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2025-02-06 10:04:50,170 - INFO: Mean error rate = 0.001 2025-02-06 10:04:50,171 - INFO: Counting read lengths ... 2025-02-06 10:05:15,596 - INFO: Mean = 103.0 bp, maximum = 150 bp. 2025-02-06 10:05:15,596 - INFO: Reads used = 20000000+20000000 2025-02-06 10:05:15,596 - INFO: Pre-reading fastq finished. 2025-02-06 10:05:15,596 - INFO: Making seed reads ... 2025-02-06 10:05:15,599 - INFO: Seed bowtie2 index existed! 2025-02-06 10:05:15,599 - INFO: Mapping reads to seed bowtie2 index ... 2025-02-06 10:11:53,070 - INFO: Mapping finished. 2025-02-06 10:11:53,073 - INFO: Seed reads made: 23-275_enriched_plastome_assembly_unclassified2/seed/embplant_pt.initial.fq (48762259 bytes) 2025-02-06 10:11:53,122 - INFO: Making seed reads finished. 2025-02-06 10:11:53,122 - INFO: Checking seed reads and parameters ... 2025-02-06 10:11:57,039 - INFO: Estimated embplant_pt-hitting base-coverage = 127.67 2025-02-06 10:11:57,954 - INFO: Setting '--max-extending-len inf' 2025-02-06 10:11:58,079 - INFO: Checking seed reads and parameters finished. 2025-02-06 10:11:58,079 - INFO: Making read index ... 2025-02-06 10:13:28,264 - INFO: 17812069 candidates in all 40000000 reads 2025-02-06 10:13:28,264 - INFO: Pre-grouping reads ... 2025-02-06 10:13:28,264 - INFO: Setting '--pre-w 101' 2025-02-06 10:13:29,047 - INFO: 200000/1117348 used/duplicated 2025-02-06 10:13:37,264 - INFO: 1814 groups made. 2025-02-06 10:13:38,079 - INFO: Making read index finished. 2025-02-06 10:13:38,079 - INFO: Extending ... 2025-02-06 10:13:38,079 - INFO: Adding initial words ... 2025-02-06 10:13:39,232 - INFO: AW 612122 2025-02-06 10:14:29,322 - INFO: Round 1: 17812069/17812069 AI 90993 AW 737330 2025-02-06 10:15:18,857 - INFO: Round 2: 17812069/17812069 AI 95141 AW 770146 2025-02-06 10:16:08,491 - INFO: Round 3: 17812069/17812069 AI 100633 AW 811928 2025-02-06 10:16:58,478 - INFO: Round 4: 17812069/17812069 AI 107501 AW 866698 2025-02-06 10:17:48,958 - INFO: Round 5: 17812069/17812069 AI 117487 AW 949290 2025-02-06 10:18:41,204 - INFO: Round 6: 17812069/17812069 AI 131219 AW 1068010 2025-02-06 10:19:33,984 - INFO: Round 7: 17812069/17812069 AI 150084 AW 1232004 2025-02-06 10:20:28,494 - INFO: Round 8: 17812069/17812069 AI 173890 AW 1434948 2025-02-06 10:21:23,657 - INFO: Round 9: 17812069/17812069 AI 197678 AW 1626548 2025-02-06 10:22:20,082 - INFO: Round 10: 17812069/17812069 AI 212378 AW 1745884 2025-02-06 10:23:16,503 - INFO: Round 11: 17812069/17812069 AI 220004 AW 1813196 2025-02-06 10:24:12,901 - INFO: Round 12: 17812069/17812069 AI 224679 AW 1859386 2025-02-06 10:25:11,255 - INFO: Round 13: 17812069/17812069 AI 227827 AW 1891044 2025-02-06 10:26:09,360 - INFO: Round 14: 17812069/17812069 AI 229756 AW 1909814 2025-02-06 10:27:07,455 - INFO: Round 15: 17812069/17812069 AI 230778 AW 1920522 2025-02-06 10:28:06,121 - INFO: Round 16: 17812069/17812069 AI 231306 AW 1926274 2025-02-06 10:29:04,891 - INFO: Round 17: 17812069/17812069 AI 231739 AW 1931040 2025-02-06 10:30:03,792 - INFO: Round 18: 17812069/17812069 AI 232025 AW 1934260 2025-02-06 10:31:02,761 - INFO: Round 19: 17812069/17812069 AI 232257 AW 1937252 2025-02-06 10:32:01,693 - INFO: Round 20: 17812069/17812069 AI 232483 AW 1939894 2025-02-06 10:33:00,192 - INFO: Round 21: 17812069/17812069 AI 232539 AW 1940338 2025-02-06 10:33:58,642 - INFO: Round 22: 17812069/17812069 AI 232539 AW 1940338 2025-02-06 10:33:58,676 - INFO: No more reads found and terminated ... 2025-02-06 10:34:25,849 - INFO: Extending finished. 2025-02-06 10:34:26,956 - INFO: Separating extended fastq file ... 2025-02-06 10:34:27,581 - INFO: Setting '-k 21,55,85,115' 2025-02-06 10:34:27,581 - INFO: Assembling using SPAdes ... 2025-02-06 10:34:27,794 - INFO: spades.py -t 1 --phred-offset 33 -1 23-275_enriched_plastome_assembly_unclassified2/extended_1_paired.fq -2 23-275_enriched_plastome_assembly_unclassified2/extended_2_paired.fq --s1 23-275_enriched_plastome_assembly_unclassified2/extended_1_unpaired.fq --s2 23-275_enriched_plastome_assembly_unclassified2/extended_2_unpaired.fq -k 21,55,85,115 -o 23-275_enriched_plastome_assembly_unclassified2/extended_spades 2025-02-06 10:36:17,814 - INFO: Insert size = 168.545, deviation = 49.1886, left quantile = 122, right quantile = 236 2025-02-06 10:36:17,815 - INFO: Assembling finished. 2025-02-06 10:36:44,580 - INFO: Slimming 23-275_enriched_plastome_assembly_unclassified2/extended_spades/K115/assembly_graph.fastg finished! 2025-02-06 10:36:44,580 - INFO: Slimming assembly graphs finished. 2025-02-06 10:36:44,581 - INFO: Extracting embplant_pt from the assemblies ... 2025-02-06 10:36:44,964 - INFO: Disentangling 23-275_enriched_plastome_assembly_unclassified2/extended_spades/K115/assembly_graph.fastg.extend-Loranth_refdata.fastg as a circular genome ... 2025-02-06 10:36:45,817 - INFO: Disentangling unsuccessful: 'Incomplete/Complicated graph: please check around EDGE_21260!' 2025-02-06 10:36:45,818 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 2025-02-06 10:36:45,818 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph. 2025-02-06 10:36:45,818 - INFO: Disentangling 23-275_enriched_plastome_assembly_unclassified2/extended_spades/K115/assembly_graph.fastg.extend-Loranth_refdata.fastg as a circular genome ... 2025-02-06 10:36:45,851 - INFO: Disentangling unsuccessful: 'No new connections.' 2025-02-06 10:36:45,852 - INFO: Disentangling 23-275_enriched_plastome_assembly_unclassified2/extended_spades/K115/assembly_graph.fastg.extend-Loranth_refdata.fastg as a/an Loranth_refdata-insufficient graph ... 2025-02-06 10:36:48,240 - INFO: Average embplant_pt kmer-coverage = 25.6 2025-02-06 10:36:48,241 - INFO: Average embplant_pt base-coverage = -239.5 2025-02-06 10:36:48,241 - INFO: Writing output ... 2025-02-06 10:36:48,254 - INFO: Writing PATH1 of embplant_pt scaffold(s) to 23-275_enriched_plastome_assembly_unclassified2/embplant_pt.K115.scaffolds.graph1.1.path_sequence.fasta 2025-02-06 10:36:48,256 - INFO: Writing GRAPH to 23-275_enriched_plastome_assembly_unclassified2/embplant_pt.K115.contigs.graph1.selected_graph.gfa 2025-02-06 10:36:48,270 - INFO: Result status of embplant_pt: 1 scaffold(s) 2025-02-06 10:36:48,347 - INFO: Writing output finished. 2025-02-06 10:36:48,348 - INFO: Please ... 2025-02-06 10:36:48,348 - INFO: load the graph file 'assembly_graph.fastg.extend-Loranth_refdata.fastg' in K115 2025-02-06 10:36:48,348 - INFO: load the CSV file 'assembly_graph.fastg.extend-Loranth_refdata.csv' in K115 2025-02-06 10:36:48,348 - INFO: visualize and confirm the incomplete result in Bandage. 2025-02-06 10:36:48,348 - INFO: If the result is nearly complete, 2025-02-06 10:36:48,348 - 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 2025-02-06 10:36:48,348 - 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! 2025-02-06 10:36:48,348 - INFO: Extracting embplant_pt from the assemblies finished. Total cost 1944.59 s Thank you!