incomplete animal_mt #164

yergol · 2022-05-06T08:56:45Z

yergol
May 6, 2022

Hi,
I try to assemble an animal mitogenome with GetOrganelle but I couldnt achieve to obtain a circular complete genome. My graph in Bandage looks like below and I attached the log file also. I tried the suggestions you added on FAQs but still it's not solved. May I hear your further suggestions? Thank you so much!

GetOrganelle v1.7.4.1

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 3.7.1 (default, Dec 14 2018, 19:28:38) [GCC 7.3.0]
PLATFORM: Linux s051 3.10.0-327.36.1.el7.x86_64 #1 SMP Sun Sep 18 13:04:29 UTC 2016 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.4.1; numpy 1.19.2; sympy 1.5.1; scipy 1.6.2
DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.10.1
GETORG_PATH=/okyanus/users/yergol/.GetOrganelle
LABEL DB: animal_mt 0.0.1
WORKING DIR: /okyanus/users/yergol
/okyanus/users/yergol/.conda/envs/yeliz/bin/get_organelle_from_reads.py -s /okyanus/users/yergol/mt10165_go/animal_mt.K115.scaffolds.graph1.1.path_sequence.fasta -1 /okyanus/users/yergol/03_trimmed_data/t10165_1P.fastq.gz -2 /okyanus/users/yergol/03_trimmed_data/t10165_2P.fastq.gz -o mt10165_go2 -w 95 -R 25 -F animal_mt

2022-05-06 10:31:24,813 - INFO: Pre-reading fastq ...
2022-05-06 10:31:24,813 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2022-05-06 10:31:24,992 - INFO: Tasting 100000+100000 reads ...
2022-05-06 10:31:48,611 - INFO: Tasting 500000+500000 reads ...
2022-05-06 10:32:09,279 - INFO: Tasting 2500000+2500000 reads ...
2022-05-06 10:33:31,421 - INFO: Estimating reads to use finished.
2022-05-06 10:33:31,422 - INFO: Unzipping reads file: /okyanus/users/yergol/03_trimmed_data/t10165_1P.fastq.gz (572236088 bytes)
2022-05-06 10:33:51,280 - INFO: Unzipping reads file: /okyanus/users/yergol/03_trimmed_data/t10165_2P.fastq.gz (563848597 bytes)
2022-05-06 10:34:11,156 - INFO: Counting read qualities ...
2022-05-06 10:34:11,284 - INFO: Identified quality encoding format = Sanger
2022-05-06 10:34:11,284 - INFO: Phred offset = 33
2022-05-06 10:34:11,285 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2022-05-06 10:34:11,316 - INFO: Mean error rate = 0.0011
2022-05-06 10:34:11,316 - INFO: Counting read lengths ...
2022-05-06 10:34:38,734 - INFO: Mean = 119.9 bp, maximum = 151 bp.
2022-05-06 10:34:38,735 - INFO: Reads used = 10129833+10129833
2022-05-06 10:34:38,736 - INFO: Pre-reading fastq finished.

2022-05-06 10:34:38,736 - INFO: Making seed reads ...
2022-05-06 10:34:38,747 - INFO: Making seed - bowtie2 index ...
2022-05-06 10:34:38,990 - INFO: Making seed - bowtie2 index finished.
2022-05-06 10:34:38,990 - INFO: Mapping reads to seed bowtie2 index ...
2022-05-06 10:38:14,834 - INFO: Mapping finished.
2022-05-06 10:38:14,836 - INFO: Seed reads made: mt10165_go2/seed/animal_mt.initial.fq (2728152 bytes)
2022-05-06 10:38:14,837 - INFO: Making seed reads finished.

2022-05-06 10:38:14,837 - INFO: Checking seed reads and parameters ...
2022-05-06 10:38:15,239 - INFO: Estimated animal_mt-hitting base-coverage = 49.19
2022-05-06 10:38:15,422 - INFO: Setting '--max-extending-len inf'
2022-05-06 10:38:15,429 - INFO: Checking seed reads and parameters finished.

2022-05-06 10:38:15,429 - INFO: Making read index ...
2022-05-06 10:40:17,110 - INFO: 13474598 candidates in all 20259666 reads
2022-05-06 10:40:17,141 - INFO: Pre-grouping reads ...
2022-05-06 10:40:17,141 - INFO: Setting '--pre-w 95'
2022-05-06 10:40:18,691 - INFO: 200000/444796 used/duplicated
2022-05-06 10:40:47,685 - INFO: 1187 groups made.
2022-05-06 10:40:50,860 - INFO: Making read index finished.

2022-05-06 10:40:50,860 - INFO: Extending ...
2022-05-06 10:40:50,860 - INFO: Adding initial words ...
2022-05-06 10:40:51,084 - INFO: AW 100242
2022-05-06 10:42:05,766 - INFO: Round 1: 13474598/13474598 AI 6651 AW 116422
2022-05-06 10:43:20,896 - INFO: Round 2: 13474598/13474598 AI 6805 AW 119846
2022-05-06 10:44:36,016 - INFO: Round 3: 13474598/13474598 AI 6834 AW 120386
2022-05-06 10:45:51,294 - INFO: Round 4: 13474598/13474598 AI 6834 AW 120386
2022-05-06 10:45:51,294 - INFO: No more reads found and terminated ...
2022-05-06 10:46:22,540 - INFO: Extending finished.

2022-05-06 10:46:22,541 - INFO: Separating extended fastq file ...
2022-05-06 10:46:22,570 - INFO: Setting '-k 21,55,85,115'
2022-05-06 10:46:22,570 - INFO: Assembling using SPAdes ...
2022-05-06 10:46:22,757 - INFO: spades.py -t 1 --phred-offset 33 -1 mt10165_go2/extended_1_paired.fq -2 mt10165_go2/extended_2_paired.fq --s1 mt10165_go2/extended_1_unpaired.fq --s2 mt10165_go2/extended_2_unpaired.fq -k 21,55,85,115 -o mt10165_go2/extended_spades
2022-05-06 10:46:35,334 - INFO: Insert size = 182.412, deviation = 38.8116, left quantile = 148, right quantile = 231
2022-05-06 10:46:35,334 - INFO: Assembling finished.

2022-05-06 10:46:47,318 - INFO: Slimming mt10165_go2/extended_spades/K115/assembly_graph.fastg finished!
2022-05-06 10:46:49,137 - INFO: Slimming mt10165_go2/extended_spades/K85/assembly_graph.fastg finished!
2022-05-06 10:46:50,930 - INFO: Slimming mt10165_go2/extended_spades/K55/assembly_graph.fastg finished!
2022-05-06 10:46:50,931 - INFO: Slimming assembly graphs finished.

2022-05-06 10:46:50,931 - INFO: Extracting animal_mt from the assemblies ...
2022-05-06 10:46:50,935 - INFO: Disentangling mt10165_go2/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2022-05-06 10:46:51,021 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_16100!'
2022-05-06 10:46:51,022 - INFO: Disentangling mt10165_go2/extended_spades/K85/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2022-05-06 10:46:51,045 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_18970!'
2022-05-06 10:46:51,045 - INFO: Disentangling mt10165_go2/extended_spades/K55/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2022-05-06 10:46:51,362 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_19340!'
2022-05-06 10:46:51,362 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ...
2022-05-06 10:46:51,362 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph.
2022-05-06 10:46:51,363 - INFO: Disentangling mt10165_go2/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2022-05-06 10:46:51,365 - INFO: Disentangling failed: 'No new connections.'
2022-05-06 10:46:51,366 - INFO: Disentangling mt10165_go2/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a/an animal_mt-insufficient graph ...
2022-05-06 10:46:52,206 - WARNING: Self-loop contig detected: Vertex_2492
2022-05-06 10:46:53,124 - INFO: Average animal_mt kmer-coverage = 12.2
2022-05-06 10:46:53,124 - INFO: Average animal_mt base-coverage = 247.6
2022-05-06 10:46:53,124 - INFO: Writing output ...
2022-05-06 10:46:53,133 - INFO: Writing PATH1 of animal_mt scaffold(s) to mt10165_go2/animal_mt.K115.scaffolds.graph1.1.path_sequence.fasta
2022-05-06 10:46:53,134 - INFO: Writing GRAPH to mt10165_go2/animal_mt.K115.contigs.graph1.selected_graph.gfa
2022-05-06 10:46:53,135 - INFO: Result status of animal_mt: 1 scaffold(s)
2022-05-06 10:46:53,242 - INFO: Writing output finished.
2022-05-06 10:46:53,243 - INFO: Please ...
2022-05-06 10:46:53,243 - INFO: load the graph file 'assembly_graph.fastg.extend-animal_mt.fastg' in K115,K85,K55
2022-05-06 10:46:53,243 - INFO: load the CSV file 'assembly_graph.fastg.extend-animal_mt.csv' in K115,K85,K55
2022-05-06 10:46:53,243 - INFO: visualize and confirm the incomplete result in Bandage.
2022-05-06 10:46:53,243 - INFO: If the result is nearly complete,
2022-05-06 10:46:53,243 - 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
2022-05-06 10:46:53,243 - 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!
2022-05-06 10:46:53,243 - INFO: Extracting animal_mt from the assemblies finished.