Visualization of chloroplast genome band age #157

wangyuhang970520 · 2022-03-25T04:28:52Z

wangyuhang970520
Mar 25, 2022

I used getorganelle to assemble the chloroplast genome. The visualization results using bandage are as follows. There seems to be a problem with the large single copy region. I hope to get the teacher's help！

GetOrganelle v1.7.5.3

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 3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:36:02) [GCC 9.3.0]
PLATFORM: Linux debian 4.19.0-18-amd64 #1 SMP Debian 4.19.208-1 (2021-09-29) x86_64
PYTHON LIBS: GetOrganelleLib 1.7.5.3; numpy 1.19.5; sympy 1.7.1; scipy 1.5.3
DEPENDENCIES: Bowtie2 2.4.5; SPAdes 3.15.4; Blast 2.12.0
GETORG_PATH=/home/j12/.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/j12/Chloroplast/bxy
/home/j12/miniconda3/envs/py36/bin/get_organelle_from_reads.py -1 bei-bobai_FDSW210309746-2r_1.fq.gz -2 bei-bobai_FDSW210309746-2r_2.fq.gz -o output_8 -R 10 -k 21,105 -F embplant_pt -t 10

2022-03-24 22:41:22,984 - INFO: Pre-reading fastq ...
2022-03-24 22:41:22,984 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2022-03-24 22:41:23,062 - INFO: Tasting 100000+100000 reads ...
2022-03-24 22:41:52,268 - INFO: Tasting 500000+500000 reads ...
2022-03-24 22:42:11,960 - INFO: Estimating reads to use finished.
2022-03-24 22:42:11,961 - INFO: Unzipping reads file: bei-bobai_FDSW210309746-2r_1.fq.gz (1194628058 bytes)
2022-03-24 22:43:23,651 - INFO: Unzipping reads file: bei-bobai_FDSW210309746-2r_2.fq.gz (1296279327 bytes)
2022-03-24 22:44:52,473 - INFO: Counting read qualities ...
2022-03-24 22:44:52,672 - INFO: Identified quality encoding format = Sanger
2022-03-24 22:44:52,673 - INFO: Phred offset = 33
2022-03-24 22:44:52,674 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2022-03-24 22:44:52,729 - INFO: Mean error rate = 0.0026
2022-03-24 22:44:52,730 - INFO: Counting read lengths ...
2022-03-24 22:46:14,403 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2022-03-24 22:46:14,458 - INFO: Reads used = 15000000+15000000
2022-03-24 22:46:14,458 - INFO: Pre-reading fastq finished.

2022-03-24 22:46:14,459 - INFO: Making seed reads ...
2022-03-24 22:46:14,470 - INFO: Seed bowtie2 index existed!
2022-03-24 22:46:14,470 - INFO: Mapping reads to seed bowtie2 index ...
2022-03-24 22:50:44,928 - INFO: Mapping finished.
2022-03-24 22:50:44,928 - INFO: Seed reads made: output_8/seed/embplant_pt.initial.fq (11558258 bytes)
2022-03-24 22:50:44,928 - INFO: Making seed reads finished.

2022-03-24 22:50:44,928 - INFO: Checking seed reads and parameters ...
2022-03-24 22:50:44,928 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2022-03-24 22:50:44,928 - INFO: If the result graph is not a circular organelle genome,
2022-03-24 22:50:44,928 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2022-03-24 22:50:48,120 - INFO: Pre-assembling mapped reads ...
2022-03-24 22:50:54,005 - INFO: Pre-assembling mapped reads finished.
2022-03-24 22:50:54,006 - INFO: Estimated embplant_pt-hitting base-coverage = 378.26
2022-03-24 22:50:54,176 - INFO: Estimated word size(s): 112
2022-03-24 22:50:54,176 - INFO: Setting '-w 112'
2022-03-24 22:50:54,176 - INFO: Setting '--max-extending-len inf'
2022-03-24 22:50:54,253 - INFO: Checking seed reads and parameters finished.

2022-03-24 22:50:54,253 - INFO: Making read index ...
2022-03-24 22:55:58,526 - INFO: 24895867 candidates in all 30000000 reads
2022-03-24 22:55:58,578 - INFO: Pre-grouping reads ...
2022-03-24 22:55:58,578 - INFO: Setting '--pre-w 112'
2022-03-24 22:56:00,854 - INFO: 200000/4116297 used/duplicated
2022-03-24 22:56:19,539 - INFO: 4193 groups made.
2022-03-24 22:56:25,245 - INFO: Making read index finished.

2022-03-24 22:56:25,245 - INFO: Extending ...
2022-03-24 22:56:25,245 - INFO: Adding initial words ...
2022-03-24 22:56:26,014 - INFO: AW 240716
2022-03-24 22:59:09,986 - INFO: Round 1: 24895867/24895867 AI 96134 AW 629340
2022-03-24 23:01:48,007 - INFO: Round 2: 24895867/24895867 AI 146214 AW 851772
2022-03-24 23:04:28,573 - INFO: Round 3: 24895867/24895867 AI 175253 AW 988056
2022-03-24 23:07:09,752 - INFO: Round 4: 24895867/24895867 AI 188671 AW 1048042
2022-03-24 23:09:51,025 - INFO: Round 5: 24895867/24895867 AI 193654 AW 1070454
2022-03-24 23:12:32,513 - INFO: Round 6: 24895867/24895867 AI 196554 AW 1082838
2022-03-24 23:15:14,029 - INFO: Round 7: 24895867/24895867 AI 199013 AW 1094598
2022-03-24 23:17:56,326 - INFO: Round 8: 24895867/24895867 AI 201462 AW 1103658
2022-03-24 23:20:38,130 - INFO: Round 9: 24895867/24895867 AI 201832 AW 1106060
2022-03-24 23:23:19,640 - INFO: Round 10: 24895867/24895867 AI 202494 AW 1111994
2022-03-24 23:23:19,641 - INFO: Hit the round limit 10 and terminated ...
2022-03-24 23:24:39,659 - INFO: Extending finished.

2022-03-24 23:24:40,388 - INFO: Separating extended fastq file ...
2022-03-24 23:24:42,077 - INFO: Setting '-k 21,105'
2022-03-24 23:24:42,077 - INFO: Assembling using SPAdes ...
2022-03-24 23:24:42,185 - INFO: spades.py -t 10 --phred-offset 33 -1 output_8/extended_1_paired.fq -2 output_8/extended_2_paired.fq --s1 output_8/extended_1_unpaired.fq --s2 output_8/extended_2_unpaired.fq -k 21,105 -o output_8/extended_spades
2022-03-24 23:25:21,229 - INFO: Insert size = 379.712, deviation = 80.7574, left quantile = 281, right quantile = 482
2022-03-24 23:25:21,229 - INFO: Assembling finished.

2022-03-24 23:25:26,119 - INFO: Slimming output_8/extended_spades/K105/assembly_graph.fastg finished!
2022-03-24 23:25:26,119 - INFO: Slimming assembly graphs finished.

2022-03-24 23:25:26,119 - INFO: Extracting embplant_pt from the assemblies ...
2022-03-24 23:25:26,120 - INFO: Disentangling output_8/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-03-24 23:25:26,540 - INFO: Vertex_153 #copy = 1
2022-03-24 23:25:26,540 - INFO: Vertex_171 #copy = 1
2022-03-24 23:25:26,540 - INFO: Vertex_179 #copy = 2
2022-03-24 23:25:26,540 - INFO: Vertex_3293 #copy = 2
2022-03-24 23:25:26,540 - INFO: Vertex_87 #copy = 1
2022-03-24 23:25:26,540 - INFO: Vertex_99 #copy = 1
2022-03-24 23:25:26,540 - INFO: Average embplant_pt kmer-coverage = 97.5
2022-03-24 23:25:26,540 - INFO: Average embplant_pt base-coverage = 317.9
2022-03-24 23:25:26,540 - INFO: Writing output ...
2022-03-24 23:25:26,595 - WARNING: More than one circular genome structure produced ...
2022-03-24 23:25:26,595 - WARNING: Please check the final result to confirm whether they are simply different in SSC direction (two flip-flop configurations)!
2022-03-24 23:25:27,089 - INFO: Detecting large repeats (>1000 bp) in PATH1 with IRs detected, Total:LSC:SSC:Repeat(bp) = 149410:83586:21240:22292
2022-03-24 23:25:27,090 - INFO: Writing PATH1 of complete embplant_pt to output_8/embplant_pt.K105.complete.graph1.1.path_sequence.fasta
2022-03-24 23:25:27,092 - INFO: Writing PATH2 of complete embplant_pt to output_8/embplant_pt.K105.complete.graph1.2.path_sequence.fasta
2022-03-24 23:25:27,092 - INFO: Writing GRAPH to output_8/embplant_pt.K105.complete.graph1.selected_graph.gfa
2022-03-24 23:25:27,169 - INFO: Result status of embplant_pt: circular genome
2022-03-24 23:25:27,261 - INFO: Please visualize output_8/extended_K105.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg using Bandage to confirm the final result.
2022-03-24 23:25:27,261 - INFO: Writing output finished.
2022-03-24 23:25:27,262 - INFO: Extracting embplant_pt from the assemblies finished.

Total cost 2645.34 s
Thank you!

Answered by Kinggerm

Mar 25, 2022

There is nothing erroneous and nothing you need to do to correct it here. You may go ahead using one of PATH1 and PATH2, which are equivalent as your final assembly,

The short brown contig is just a pair of directed repeats in the linear form of as,

----- brown --- cyan --- brown ----

which rolls up in the assembly graph as

            cyan
          /          \
          \          /
----- (brown)*2 -----

Please also refer to

View full answer

Kinggerm · 2022-03-25T20:15:20Z

Kinggerm
Mar 25, 2022
Maintainer

There is nothing erroneous and nothing you need to do to correct it here. You may go ahead using one of PATH1 and PATH2, which are equivalent as your final assembly,

The short brown contig is just a pair of directed repeats in the linear form of as,

----- brown --- cyan --- brown ----

which rolls up in the assembly graph as

            cyan
          /          \
          \          /
----- (brown)*2 -----

Please also refer to

1 reply

wangyuhang970520 Mar 26, 2022
Author

ok, thanks , I got it

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Visualization of chloroplast genome band age #157

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Kinggerm Mar 25, 2022 Maintainer

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