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 3.8.18 (default, Sep 11 2023, 13:40:15) [GCC 11.2.0] PLATFORM: Linux fierst-lab 5.15.0-92-generic #102-Ubuntu SMP Wed Jan 10 09:33:48 UTC 2024 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.24.3; sympy 1.11.1; scipy 1.10.1 DEPENDENCIES: Bowtie2 2.4.1; SPAdes 3.13.1; Blast 2.5.0 GETORG_PATH=/home/juaguila/.GetOrganelle SEED DB: animal_mt 0.0.1 LABEL DB: animal_mt 0.0.1 WORKING DIR: /DataDrive/juaguila/Rohits /home/juaguila/miniconda3/envs/MT_DNA/bin/get_organelle_from_reads.py -1 E150014155_L01_117_1.fq.gz -2 E150014155_L01_117_2.fq.gz -t 12 -F animal_mt -o 117 --reduce-reads-for-coverage inf --max-reads inf 2024-03-27 16:23:26,957 - INFO: Pre-reading fastq ... 2024-03-27 16:23:26,958 - INFO: Unzipping reads file: E150014155_L01_117_1.fq.gz (3194354096 bytes) 2024-03-27 16:24:43,074 - INFO: Unzipping reads file: E150014155_L01_117_2.fq.gz (3130190696 bytes) 2024-03-27 16:25:58,315 - INFO: Counting read qualities ... 2024-03-27 16:25:58,491 - INFO: Identified quality encoding format = Sanger 2024-03-27 16:25:58,491 - INFO: Phred offset = 33 2024-03-27 16:25:58,493 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2024-03-27 16:25:58,613 - INFO: Mean error rate = 0.0027 2024-03-27 16:25:58,614 - INFO: Counting read lengths ... 2024-03-27 16:26:44,317 - INFO: Mean = 150.0 bp, maximum = 150 bp. 2024-03-27 16:26:44,318 - INFO: Reads used = 24150004+24150004 2024-03-27 16:26:44,318 - INFO: Pre-reading fastq finished. 2024-03-27 16:26:44,318 - INFO: Making seed reads ... 2024-03-27 16:26:44,318 - INFO: Seed bowtie2 index existed! 2024-03-27 16:26:44,318 - INFO: Mapping reads to seed bowtie2 index ... 2024-03-27 16:30:00,764 - INFO: Mapping finished. 2024-03-27 16:30:00,765 - INFO: Seed reads made: 117/seed/animal_mt.initial.fq (2100000 bytes) 2024-03-27 16:30:00,766 - INFO: Making seed reads finished. 2024-03-27 16:30:00,766 - INFO: Checking seed reads and parameters ... 2024-03-27 16:30:00,767 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s). 2024-03-27 16:30:00,767 - INFO: If the result graph is not a circular organelle genome, 2024-03-27 16:30:00,767 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run. 2024-03-27 16:30:02,807 - INFO: Pre-assembling mapped reads ... 2024-03-27 16:30:08,031 - INFO: Pre-assembling mapped reads finished. 2024-03-27 16:30:08,032 - INFO: Estimated animal_mt-hitting base-coverage = 269.92 2024-03-27 16:30:08,233 - INFO: Estimated word size(s): 114 2024-03-27 16:30:08,233 - INFO: Setting '-w 114' 2024-03-27 16:30:08,234 - INFO: Setting '--max-extending-len inf' 2024-03-27 16:30:08,372 - INFO: Checking seed reads and parameters finished. 2024-03-27 16:30:08,372 - INFO: Making read index ... 2024-03-27 16:34:46,695 - INFO: 45657691 candidates in all 48300008 reads 2024-03-27 16:34:46,695 - INFO: Pre-grouping reads ... 2024-03-27 16:34:46,695 - INFO: Setting '--pre-w 114' 2024-03-27 16:34:49,961 - INFO: 200000/1747847 used/duplicated 2024-03-27 16:35:00,902 - INFO: 12637 groups made. 2024-03-27 16:35:04,060 - INFO: Making read index finished. 2024-03-27 16:35:04,060 - INFO: Extending ... 2024-03-27 16:35:04,060 - INFO: Adding initial words ... 2024-03-27 16:35:04,187 - INFO: AW 92538 2024-03-27 16:37:55,630 - INFO: Round 1: 45657691/45657691 AI 54622 AW 390450 2024-03-27 16:41:02,394 - INFO: Round 2: 45657691/45657691 AI 58473 AW 449650 2024-03-27 16:44:14,597 - INFO: Round 3: 45657691/45657691 AI 62064 AW 476574 2024-03-27 16:47:33,646 - INFO: Round 4: 45657691/45657691 AI 63761 AW 489984 2024-03-27 16:50:56,944 - INFO: Round 5: 45657691/45657691 AI 65127 AW 502066 2024-03-27 16:54:23,263 - INFO: Round 6: 45657691/45657691 AI 66369 AW 513360 2024-03-27 16:57:41,445 - INFO: Round 7: 45657691/45657691 AI 69106 AW 540868 2024-03-27 17:01:00,363 - INFO: Round 8: 45657691/45657691 AI 88394 AW 699520 2024-03-27 17:04:27,730 - INFO: Round 9: 45657691/45657691 AI 112040 AW 902044 2024-03-27 17:08:02,133 - INFO: Round 10: 45657691/45657691 AI 140698 AW 1154462 2024-03-27 17:08:02,133 - INFO: Hit the round limit 10 and terminated ... 2024-03-27 17:08:54,999 - INFO: Extending finished. 2024-03-27 17:08:56,160 - INFO: Separating extended fastq file ... 2024-03-27 17:08:56,569 - INFO: Setting '-k 21,55,85,115' 2024-03-27 17:08:56,570 - INFO: Assembling using SPAdes ... 2024-03-27 17:08:56,598 - INFO: spades.py -t 12 --phred-offset 33 -1 117/extended_1_paired.fq -2 117/extended_2_paired.fq --s1 117/extended_1_unpaired.fq --s2 117/extended_2_unpaired.fq -k 21,55,85,115 -o 117/extended_spades 2024-03-27 17:09:26,961 - INFO: Insert size = 244.486, deviation = 51.8878, left quantile = 181, right quantile = 314 2024-03-27 17:09:26,961 - INFO: Assembling finished. 2024-03-27 17:09:28,116 - INFO: Slimming 117/extended_spades/K115/assembly_graph.fastg finished! 2024-03-27 17:09:28,116 - INFO: Slimming assembly graphs finished. 2024-03-27 17:09:28,116 - INFO: Extracting animal_mt from the assemblies ... 2024-03-27 17:09:28,116 - INFO: Disentangling 117/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ... 2024-03-27 17:09:28,120 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_109174!' 2024-03-27 17:09:28,121 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 2024-03-27 17:09:28,121 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph. 2024-03-27 17:09:28,121 - INFO: Disentangling 117/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ... 2024-03-27 17:09:28,121 - INFO: Disentangling failed: 'No new connections.' 2024-03-27 17:09:28,121 - INFO: Disentangling 117/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a/an animal_mt-insufficient graph ... 2024-03-27 17:09:28,130 - INFO: Average animal_mt coverage = 232.8 2024-03-27 17:09:28,130 - INFO: Average animal_mt base-coverage = 969.9 2024-03-27 17:09:28,130 - INFO: Writing output ... 2024-03-27 17:09:28,135 - INFO: Writing PATH1 of animal_mt scaffold(s) to 117/animal_mt.K115.scaffolds.graph1.1.path_sequence.fasta 2024-03-27 17:09:28,136 - INFO: Writing GRAPH to 117/animal_mt.K115.contigs.graph1.selected_graph.gfa 2024-03-27 17:09:28,136 - INFO: Result status of animal_mt: 1 scaffold(s) 2024-03-27 17:09:28,142 - INFO: Writing output finished. 2024-03-27 17:09:28,146 - INFO: Please ... 2024-03-27 17:09:28,148 - INFO: load the graph file 'assembly_graph.fastg.extend-animal_mt.fastg' in K115 2024-03-27 17:09:28,150 - INFO: load the CSV file 'assembly_graph.fastg.extend-animal_mt.csv' in K115 2024-03-27 17:09:28,151 - INFO: visualize and confirm the incomplete result in Bandage. 2024-03-27 17:09:28,152 - INFO: If the result is nearly complete, 2024-03-27 17:09:28,153 - 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 2024-03-27 17:09:28,154 - 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! 2024-03-27 17:09:28,156 - INFO: Extracting animal_mt from the assemblies finished. Total cost 2762.15 s Thank you!