GetOrganelle v1.7.6.1

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 3.8.13 (default, Mar 28 2022, 11:38:47)  [GCC 7.5.0]
PLATFORM: Linux mju-oceanpbi 4.18.0-373.el8.x86_64 #1 SMP Tue Mar 22 15:11:47 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.6.1; numpy 1.23.1; sympy 1.10.1; scipy 1.9.1
DEPENDENCIES: Bowtie2 2.4.1; SPAdes 3.13.1; Blast 2.12.0
GETORG_PATH=/home/dahome/teachers/chenyanqiong/.GetOrganelle
SEED  DB: embplant_pt 0.0.0; embplant_mt 0.0.1.minima
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /home/dahome/teachers/chenyanqiong/project/cpAssemble/dapiaoX1
/home/dahome/teachers/chenyanqiong/miniconda3/envs/getorganelle/bin/get_organelle_from_reads.py -1 X1_1.clean.fq.gz -2 X1_2.clean.fq.gz -o dapiao -R 10 -k 75,85,95,105 -F embplant_pt

2022-10-25 21:11:59,377 - INFO: Pre-reading fastq ...
2022-10-25 21:11:59,378 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2022-10-25 21:11:59,631 - INFO: Tasting 100000+100000 reads ...
2022-10-25 21:12:33,759 - INFO: Estimating reads to use finished.
2022-10-25 21:12:33,761 - INFO: Unzipping reads file: X1_1.clean.fq.gz (1298017186 bytes)
2022-10-25 21:13:16,727 - INFO: Unzipping reads file: X1_2.clean.fq.gz (1378963717 bytes)
2022-10-25 21:13:55,242 - INFO: Counting read qualities ...
2022-10-25 21:13:56,744 - INFO: Identified quality encoding format = Sanger
2022-10-25 21:13:56,744 - INFO: Phred offset = 33
2022-10-25 21:13:56,747 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2022-10-25 21:13:56,804 - INFO: Mean error rate = 0.0024
2022-10-25 21:13:56,805 - INFO: Counting read lengths ...
2022-10-25 21:14:52,145 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2022-10-25 21:14:52,148 - INFO: Reads used = 15000000+15000000
2022-10-25 21:14:52,148 - INFO: Pre-reading fastq finished.

2022-10-25 21:14:52,148 - INFO: Making seed reads ...
2022-10-25 21:14:52,151 - INFO: Seed bowtie2 index existed!
2022-10-25 21:14:52,151 - INFO: Mapping reads to seed bowtie2 index ...
2022-10-25 21:35:58,312 - INFO: Mapping finished.
2022-10-25 21:35:58,313 - INFO: Seed reads made: dapiao/seed/embplant_pt.initial.fq (222193727 bytes)
2022-10-25 21:35:58,313 - INFO: Making seed reads finished.

2022-10-25 21:35:58,313 - INFO: Checking seed reads and parameters ...
2022-10-25 21:35:58,313 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2022-10-25 21:35:58,313 - INFO: If the result graph is not a circular organelle genome, 
2022-10-25 21:35:58,314 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2022-10-25 21:36:30,528 - INFO: Pre-assembling mapped reads ...
2022-10-25 21:38:06,021 - INFO: Pre-assembling mapped reads finished.
2022-10-25 21:38:06,022 - INFO: Estimated embplant_pt-hitting base-coverage = 766.70
2022-10-25 21:38:06,534 - INFO: Reads reduced to = 9782193+9782193
2022-10-25 21:38:06,534 - INFO: Adjusting expected embplant_pt base coverage to 500.00
2022-10-25 21:38:06,535 - INFO: Estimated word size(s): 112
2022-10-25 21:38:06,535 - INFO: Setting '-w 112'
2022-10-25 21:38:06,535 - INFO: Setting '--max-extending-len inf'
2022-10-25 21:38:07,604 - INFO: Checking seed reads and parameters finished.

2022-10-25 21:38:07,605 - INFO: Making read index ...
2022-10-25 21:39:14,560 - INFO: For dapiao/1-X1_1.clean.fq.gz.fastq, only top 9782193 reads are used in downstream analysis.
2022-10-25 21:40:25,598 - INFO: For dapiao/2-X1_2.clean.fq.gz.fastq, only top 9782193 reads are used in downstream analysis.
2022-10-25 21:40:42,812 - INFO: 14775228 candidates in all 19564386 reads
2022-10-25 21:40:42,812 - INFO: Pre-grouping reads ...
2022-10-25 21:40:42,812 - INFO: Setting '--pre-w 112'
2022-10-25 21:40:44,428 - INFO: 200000/3236638 used/duplicated
2022-10-25 21:41:03,428 - INFO: 2880 groups made.
2022-10-25 21:41:05,286 - INFO: Making read index finished.

2022-10-25 21:41:05,286 - INFO: Extending ...
2022-10-25 21:41:05,286 - INFO: Adding initial words ...
2022-10-25 21:41:26,589 - INFO: AW 5355048
2022-10-25 21:43:13,962 - INFO: Round 1: 14775228/14775228 AI 243268 AW 5726030
2022-10-25 21:44:43,312 - INFO: Round 2: 14775228/14775228 AI 247825 AW 5764176
2022-10-25 21:46:16,038 - INFO: Round 3: 14775228/14775228 AI 248017 AW 5768148
2022-10-25 21:47:53,836 - INFO: Round 4: 14775228/14775228 AI 248055 AW 5768958
2022-10-25 21:49:21,330 - INFO: Round 5: 14775228/14775228 AI 248095 AW 5769690
2022-10-25 21:51:19,029 - INFO: Round 6: 14775228/14775228 AI 248126 AW 5770274
2022-10-25 21:52:48,373 - INFO: Round 7: 14775228/14775228 AI 248146 AW 5770532
2022-10-25 21:54:20,394 - INFO: Round 8: 14775228/14775228 AI 248158 AW 5770748
2022-10-25 21:55:57,772 - INFO: Round 9: 14775228/14775228 AI 248165 AW 5770872
2022-10-25 21:57:30,790 - INFO: Round 10: 14775228/14775228 AI 248167 AW 5770940
2022-10-25 21:57:30,792 - INFO: Hit the round limit 10 and terminated ...
2022-10-25 21:58:18,218 - INFO: Extending finished.

2022-10-25 21:58:20,137 - INFO: Separating extended fastq file ... 
2022-10-25 21:58:22,895 - INFO: Setting '-k 75,85,95,105'
2022-10-25 21:58:22,896 - INFO: Assembling using SPAdes ...
2022-10-25 21:58:23,154 - INFO: spades.py -t 1  --phred-offset 33 -1 dapiao/extended_1_paired.fq -2 dapiao/extended_2_paired.fq --s1 dapiao/extended_1_unpaired.fq --s2 dapiao/extended_2_unpaired.fq -k 75,85,95,105 -o dapiao/extended_spades
2022-10-25 22:05:12,968 - INFO: Insert size = 361.829, deviation = 72.258, left quantile = 270, right quantile = 454
2022-10-25 22:05:12,969 - INFO: Assembling finished.

2022-10-25 22:05:29,248 - INFO: Slimming dapiao/extended_spades/K105/assembly_graph.fastg finished!
2022-10-25 22:05:29,248 - INFO: Slimming assembly graphs finished.

2022-10-25 22:05:29,249 - INFO: Extracting embplant_pt from the assemblies ...
2022-10-25 22:05:29,251 - INFO: Disentangling dapiao/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 
2022-10-25 22:05:29,274 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2022-10-25 22:05:29,275 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 
2022-10-25 22:05:29,275 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph.
2022-10-25 22:05:29,275 - INFO: Disentangling dapiao/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ... 
2022-10-25 22:05:29,297 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2022-10-25 22:05:29,298 - INFO: Disentangling dapiao/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a/an embplant_pt-insufficient graph ... 
2022-10-25 22:05:29,567 - INFO: Average embplant_pt kmer-coverage = 172.4
2022-10-25 22:05:29,567 - INFO: Average embplant_pt base-coverage = 562.2
2022-10-25 22:05:29,567 - INFO: Writing output ...
2022-10-25 22:05:29,709 - INFO: Writing PATH1 of embplant_pt scaffold(s) to dapiao/embplant_pt.K105.scaffolds.graph1.1.path_sequence.fasta
2022-10-25 22:05:29,711 - INFO: Writing GRAPH to dapiao/embplant_pt.K105.contigs.graph1.selected_graph.gfa
2022-10-25 22:05:29,712 - INFO: Result status of embplant_pt: 10 scaffold(s)
2022-10-25 22:05:30,140 - INFO: Writing output finished.
2022-10-25 22:05:30,141 - INFO: Please ...
2022-10-25 22:05:30,141 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg' in K105
2022-10-25 22:05:30,141 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K105
2022-10-25 22:05:30,141 - INFO: visualize and confirm the incomplete result in Bandage.
2022-10-25 22:05:30,141 - INFO: If the result is nearly complete, 
2022-10-25 22:05:30,141 - 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
2022-10-25 22:05:30,141 - 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!
2022-10-25 22:05:30,141 - INFO: Extracting embplant_pt from the assemblies finished.


Total cost 3224.17 s
Thank you!