Visualization of chloroplast genome assembly results #170

wangyuhang970520 · 2022-05-09T02:08:23Z

wangyuhang970520
May 9, 2022

These are the chloroplast assembly results of my two samples. There was no error in the assembly process and the assembly was successful into a ring, but his visual results do not look so normal. I hope teachers and students can give guidance and suggestions.

The following is my logfile

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 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0]
PLATFORM: Linux ubuntu 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.5.3; numpy 1.22.3; sympy 1.10.1; scipy 1.8.0
DEPENDENCIES: Bowtie2 2.4.5; SPAdes 3.13.0; 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
/home/j12/miniconda3/envs/py39/bin/get_organelle_from_reads.py -1 19_1.clean.fq.gz -2 19_2.clean.fq.gz -o lh19_output -R 50 -k 21,45,65,85,105 -F embplant_pt -t 10

2022-05-07 01:15:31,559 - INFO: Pre-reading fastq ...
2022-05-07 01:15:31,559 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2022-05-07 01:15:31,693 - INFO: Tasting 100000+100000 reads ...
2022-05-07 01:15:40,991 - INFO: Tasting 500000+500000 reads ...
2022-05-07 01:16:03,392 - INFO: Estimating reads to use finished.
2022-05-07 01:16:03,392 - INFO: Unzipping reads file: 19_1.clean.fq.gz (1279330098 bytes)
2022-05-07 01:17:25,578 - INFO: Unzipping reads file: 19_2.clean.fq.gz (1354707986 bytes)
2022-05-07 01:18:20,089 - INFO: Counting read qualities ...
2022-05-07 01:18:20,305 - INFO: Identified quality encoding format = Sanger
2022-05-07 01:18:20,305 - INFO: Phred offset = 33
2022-05-07 01:18:20,306 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2022-05-07 01:18:20,366 - INFO: Mean error rate = 0.0025
2022-05-07 01:18:20,367 - INFO: Counting read lengths ...
2022-05-07 01:19:55,635 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2022-05-07 01:19:55,637 - INFO: Reads used = 15000000+15000000
2022-05-07 01:19:55,637 - INFO: Pre-reading fastq finished.

2022-05-07 01:19:55,637 - INFO: Making seed reads ...
2022-05-07 01:19:55,638 - INFO: Seed bowtie2 index existed!
2022-05-07 01:19:55,638 - INFO: Mapping reads to seed bowtie2 index ...
2022-05-07 01:24:31,664 - INFO: Mapping finished.
2022-05-07 01:24:31,666 - INFO: Seed reads made: lh19_output/seed/embplant_pt.initial.fq (84263756 bytes)
2022-05-07 01:24:31,667 - INFO: Making seed reads finished.

2022-05-07 01:24:31,667 - INFO: Checking seed reads and parameters ...
2022-05-07 01:24:31,667 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2022-05-07 01:24:31,667 - INFO: If the result graph is not a circular organelle genome,
2022-05-07 01:24:31,667 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2022-05-07 01:24:42,482 - INFO: Pre-assembling mapped reads ...
2022-05-07 01:24:57,617 - INFO: Pre-assembling mapped reads finished.
2022-05-07 01:24:57,618 - INFO: Estimated embplant_pt-hitting base-coverage = 239.50
2022-05-07 01:24:57,908 - INFO: Estimated word size(s): 112
2022-05-07 01:24:57,908 - INFO: Setting '-w 112'
2022-05-07 01:24:57,908 - INFO: Setting '--max-extending-len inf'
2022-05-07 01:24:58,239 - INFO: Checking seed reads and parameters finished.

2022-05-07 01:24:58,239 - INFO: Making read index ...
2022-05-07 01:29:18,373 - INFO: 24791654 candidates in all 30000000 reads
2022-05-07 01:29:18,377 - INFO: Pre-grouping reads ...
2022-05-07 01:29:18,381 - INFO: Setting '--pre-w 112'
2022-05-07 01:29:20,964 - INFO: 200000/4233856 used/duplicated
2022-05-07 01:29:41,676 - INFO: 4070 groups made.
2022-05-07 01:29:44,616 - INFO: Making read index finished.

2022-05-07 01:29:44,617 - INFO: Extending ...
2022-05-07 01:29:44,617 - INFO: Adding initial words ...
2022-05-07 01:29:51,308 - INFO: AW 1763134
2022-05-07 01:32:30,195 - INFO: Round 1: 24791654/24791654 AI 168068 AW 1865590
2022-05-07 01:35:03,883 - INFO: Round 2: 24791654/24791654 AI 170103 AW 1875744
2022-05-07 01:37:38,021 - INFO: Round 3: 24791654/24791654 AI 170584 AW 1879854
2022-05-07 01:40:11,779 - INFO: Round 4: 24791654/24791654 AI 170961 AW 1883316
2022-05-07 01:42:45,564 - INFO: Round 5: 24791654/24791654 AI 171324 AW 1886724
2022-05-07 01:45:19,381 - INFO: Round 6: 24791654/24791654 AI 171754 AW 1890850
2022-05-07 01:47:53,334 - INFO: Round 7: 24791654/24791654 AI 172280 AW 1895474
2022-05-07 01:50:27,370 - INFO: Round 8: 24791654/24791654 AI 172781 AW 1899860
2022-05-07 01:53:03,341 - INFO: Round 9: 24791654/24791654 AI 173256 AW 1904510
2022-05-07 01:55:39,319 - INFO: Round 10: 24791654/24791654 AI 173665 AW 1908040
2022-05-07 01:58:15,616 - INFO: Round 11: 24791654/24791654 AI 174128 AW 1912148
2022-05-07 02:00:49,929 - INFO: Round 12: 24791654/24791654 AI 174590 AW 1916608
2022-05-07 02:03:23,917 - INFO: Round 13: 24791654/24791654 AI 175082 AW 1921612
2022-05-07 02:05:58,179 - INFO: Round 14: 24791654/24791654 AI 175580 AW 1926282
2022-05-07 02:08:32,523 - INFO: Round 15: 24791654/24791654 AI 176081 AW 1931144
2022-05-07 02:11:06,784 - INFO: Round 16: 24791654/24791654 AI 176683 AW 1936512
2022-05-07 02:13:40,936 - INFO: Round 17: 24791654/24791654 AI 177263 AW 1941704
2022-05-07 02:16:16,537 - INFO: Round 18: 24791654/24791654 AI 177745 AW 1946614
2022-05-07 02:18:52,130 - INFO: Round 19: 24791654/24791654 AI 178180 AW 1950598
2022-05-07 02:21:27,981 - INFO: Round 20: 24791654/24791654 AI 178728 AW 1955640
2022-05-07 02:24:03,404 - INFO: Round 21: 24791654/24791654 AI 179244 AW 1960322
2022-05-07 02:26:38,245 - INFO: Round 22: 24791654/24791654 AI 179723 AW 1964996
2022-05-07 02:29:12,718 - INFO: Round 23: 24791654/24791654 AI 180102 AW 1968796
2022-05-07 02:31:47,056 - INFO: Round 24: 24791654/24791654 AI 180577 AW 1973558
2022-05-07 02:34:21,656 - INFO: Round 25: 24791654/24791654 AI 181014 AW 1977798
2022-05-07 02:36:56,662 - INFO: Round 26: 24791654/24791654 AI 181452 AW 1981834
2022-05-07 02:39:31,409 - INFO: Round 27: 24791654/24791654 AI 182008 AW 1987422
2022-05-07 02:42:06,374 - INFO: Round 28: 24791654/24791654 AI 182515 AW 1991914
2022-05-07 02:44:41,659 - INFO: Round 29: 24791654/24791654 AI 182948 AW 1995934
2022-05-07 02:47:17,399 - INFO: Round 30: 24791654/24791654 AI 183362 AW 1999916
2022-05-07 02:49:52,965 - INFO: Round 31: 24791654/24791654 AI 183769 AW 2004458
2022-05-07 02:52:28,813 - INFO: Round 32: 24791654/24791654 AI 184229 AW 2008676
2022-05-07 02:55:04,746 - INFO: Round 33: 24791654/24791654 AI 184669 AW 2012938
2022-05-07 02:57:40,636 - INFO: Round 34: 24791654/24791654 AI 185076 AW 2017322
2022-05-07 03:00:16,335 - INFO: Round 35: 24791654/24791654 AI 185554 AW 2021830
2022-05-07 03:02:52,592 - INFO: Round 36: 24791654/24791654 AI 185994 AW 2025676
2022-05-07 03:05:28,699 - INFO: Round 37: 24791654/24791654 AI 186502 AW 2030562
2022-05-07 03:08:04,514 - INFO: Round 38: 24791654/24791654 AI 186957 AW 2034234
2022-05-07 03:10:40,129 - INFO: Round 39: 24791654/24791654 AI 187331 AW 2038116
2022-05-07 03:13:15,378 - INFO: Round 40: 24791654/24791654 AI 187937 AW 2043522
2022-05-07 03:15:50,726 - INFO: Round 41: 24791654/24791654 AI 188556 AW 2049058
2022-05-07 03:18:26,352 - INFO: Round 42: 24791654/24791654 AI 189161 AW 2053636
2022-05-07 03:21:01,869 - INFO: Round 43: 24791654/24791654 AI 189630 AW 2057514
2022-05-07 03:23:37,368 - INFO: Round 44: 24791654/24791654 AI 190045 AW 2060870
2022-05-07 03:26:13,226 - INFO: Round 45: 24791654/24791654 AI 190338 AW 2063604
2022-05-07 03:28:49,984 - INFO: Round 46: 24791654/24791654 AI 190564 AW 2065772
2022-05-07 03:31:27,667 - INFO: Round 47: 24791654/24791654 AI 190896 AW 2069414
2022-05-07 03:34:05,308 - INFO: Round 48: 24791654/24791654 AI 191272 AW 2073022
2022-05-07 03:36:43,107 - INFO: Round 49: 24791654/24791654 AI 191502 AW 2075242
2022-05-07 03:39:20,791 - INFO: Round 50: 24791654/24791654 AI 191769 AW 2078020
2022-05-07 03:39:20,791 - INFO: Hit the round limit 50 and terminated ...
2022-05-07 03:40:44,993 - INFO: Extending finished.

2022-05-07 03:40:46,172 - INFO: Separating extended fastq file ...
2022-05-07 03:40:47,096 - INFO: Setting '-k 21,45,65,85,105'
2022-05-07 03:40:47,096 - INFO: Assembling using SPAdes ...
2022-05-07 03:40:47,174 - INFO: spades.py -t 10 --phred-offset 33 -1 lh19_output/extended_1_paired.fq -2 lh19_output/extended_2_paired.fq --s1 lh19_output/extended_1_unpaired.fq --s2 lh19_output/extended_2_unpaired.fq -k 21,45,65,85,105 -o lh19_output/extended_spades
2022-05-07 03:42:03,518 - INFO: Insert size = 373.847, deviation = 73.759, left quantile = 284, right quantile = 467
2022-05-07 03:42:03,518 - INFO: Assembling finished.

2022-05-07 03:42:07,675 - INFO: Slimming lh19_output/extended_spades/K105/assembly_graph.fastg finished!
2022-05-07 03:42:08,815 - INFO: Slimming lh19_output/extended_spades/K85/assembly_graph.fastg finished!
2022-05-07 03:42:09,954 - INFO: Slimming lh19_output/extended_spades/K65/assembly_graph.fastg finished!
2022-05-07 03:42:11,091 - INFO: Slimming lh19_output/extended_spades/K45/assembly_graph.fastg finished!
2022-05-07 03:42:11,092 - INFO: Slimming assembly graphs finished.

2022-05-07 03:42:11,092 - INFO: Extracting embplant_pt from the assemblies ...
2022-05-07 03:42:11,092 - INFO: Disentangling lh19_output/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-05-07 03:42:11,473 - INFO: Vertex_50154_50130_50148_48512_50142_50170_47738 #copy = 1
2022-05-07 03:42:11,473 - INFO: Vertex_50180 #copy = 1
2022-05-07 03:42:11,473 - INFO: Vertex_50200 #copy = 2
2022-05-07 03:42:11,474 - INFO: Average embplant_pt kmer-coverage = 78.2
2022-05-07 03:42:11,474 - INFO: Average embplant_pt base-coverage = 254.9
2022-05-07 03:42:11,474 - INFO: Writing output ...
2022-05-07 03:42:11,533 - WARNING: More than one circular genome structure produced ...
2022-05-07 03:42:11,533 - WARNING: Please check the final result to confirm whether they are simply different in SSC direction (two flip-flop configurations)!
2022-05-07 03:42:12,122 - INFO: Detecting large repeats (>1000 bp) in PATH1 with IRs detected, Total:LSC:SSC:Repeat(bp) = 151148:82888:18338:24961
2022-05-07 03:42:12,122 - INFO: Writing PATH1 of complete embplant_pt to lh19_output/embplant_pt.K105.complete.graph1.1.path_sequence.fasta
2022-05-07 03:42:12,125 - INFO: Writing PATH2 of complete embplant_pt to lh19_output/embplant_pt.K105.complete.graph1.2.path_sequence.fasta
2022-05-07 03:42:12,125 - INFO: Writing GRAPH to lh19_output/embplant_pt.K105.complete.graph1.selected_graph.gfa
2022-05-07 03:42:12,178 - INFO: Result status of embplant_pt: circular genome
2022-05-07 03:42:12,238 - INFO: Please visualize lh19_output/extended_K105.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg using Bandage to confirm the final result.
2022-05-07 03:42:12,238 - INFO: Writing output finished.
2022-05-07 03:42:12,239 - INFO: Extracting embplant_pt from the assemblies finished.

Total cost 8806.57 s
Thank you!

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 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0]
PLATFORM: Linux ubuntu 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.5.3; numpy 1.22.3; sympy 1.10.1; scipy 1.8.0
DEPENDENCIES: Bowtie2 2.4.5; SPAdes 3.13.0; 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
/home/j12/miniconda3/envs/py39/bin/get_organelle_from_reads.py -1 4_1.clean.fq.gz -2 4_2.clean.fq.gz -o lh4_output -R 50 -k 21,45,65,85,105 -F embplant_pt -t 10

2022-05-06 06:38:40,317 - INFO: Pre-reading fastq ...
2022-05-06 06:38:40,317 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2022-05-06 06:38:40,441 - INFO: Tasting 100000+100000 reads ...
2022-05-06 06:38:50,681 - INFO: Estimating reads to use finished.
2022-05-06 06:38:50,681 - INFO: Unzipping reads file: 4_1.clean.fq.gz (1243125259 bytes)
2022-05-06 06:40:33,831 - INFO: Unzipping reads file: 4_2.clean.fq.gz (1312317327 bytes)
2022-05-06 06:41:54,932 - INFO: Counting read qualities ...
2022-05-06 06:41:55,125 - INFO: Identified quality encoding format = Sanger
2022-05-06 06:41:55,126 - INFO: Phred offset = 33
2022-05-06 06:41:55,127 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2022-05-06 06:41:55,175 - INFO: Mean error rate = 0.0024
2022-05-06 06:41:55,177 - INFO: Counting read lengths ...
2022-05-06 06:43:31,439 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2022-05-06 06:43:31,440 - INFO: Reads used = 15000000+15000000
2022-05-06 06:43:31,440 - INFO: Pre-reading fastq finished.

2022-05-06 06:43:31,440 - INFO: Making seed reads ...
2022-05-06 06:43:31,440 - INFO: Seed bowtie2 index existed!
2022-05-06 06:43:31,440 - INFO: Mapping reads to seed bowtie2 index ...
2022-05-06 06:48:32,755 - INFO: Mapping finished.
2022-05-06 06:48:32,767 - INFO: Seed reads made: lh4_output/seed/embplant_pt.initial.fq (195389777 bytes)
2022-05-06 06:48:32,768 - INFO: Making seed reads finished.

2022-05-06 06:48:32,768 - INFO: Checking seed reads and parameters ...
2022-05-06 06:48:32,768 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2022-05-06 06:48:32,768 - INFO: If the result graph is not a circular organelle genome,
2022-05-06 06:48:32,768 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2022-05-06 06:48:55,626 - INFO: Pre-assembling mapped reads ...
2022-05-06 06:49:14,857 - INFO: Pre-assembling mapped reads finished.
2022-05-06 06:49:14,858 - INFO: Estimated embplant_pt-hitting base-coverage = 551.02
2022-05-06 06:49:15,185 - INFO: Reads reduced to = 13611105+13611105
2022-05-06 06:49:15,186 - INFO: Adjusting expected embplant_pt base coverage to 500.00
2022-05-06 06:49:15,186 - INFO: Estimated word size(s): 112
2022-05-06 06:49:15,186 - INFO: Setting '-w 112'
2022-05-06 06:49:15,186 - INFO: Setting '--max-extending-len inf'
2022-05-06 06:49:15,890 - INFO: Checking seed reads and parameters finished.

2022-05-06 06:49:15,890 - INFO: Making read index ...
2022-05-06 06:51:06,764 - INFO: For lh4_output/1-4_1.clean.fq.gz.fastq, only top 13611105 reads are used in downstream analysis.
2022-05-06 06:52:58,452 - INFO: For lh4_output/2-4_2.clean.fq.gz.fastq, only top 13611105 reads are used in downstream analysis.
2022-05-06 06:53:15,409 - INFO: 21628749 candidates in all 27222210 reads
2022-05-06 06:53:15,410 - INFO: Pre-grouping reads ...
2022-05-06 06:53:15,410 - INFO: Setting '--pre-w 112'
2022-05-06 06:53:17,655 - INFO: 200000/4335581 used/duplicated
2022-05-06 06:53:34,026 - INFO: 4405 groups made.
2022-05-06 06:53:36,843 - INFO: Making read index finished.

2022-05-06 06:53:36,843 - INFO: Extending ...
2022-05-06 06:53:36,843 - INFO: Adding initial words ...
2022-05-06 06:53:53,997 - INFO: AW 3303424
2022-05-06 06:56:16,128 - INFO: Round 1: 21628749/21628749 AI 257773 AW 3473896
2022-05-06 06:58:21,573 - INFO: Round 2: 21628749/21628749 AI 259544 AW 3489286
2022-05-06 07:00:27,461 - INFO: Round 3: 21628749/21628749 AI 260275 AW 3496072
2022-05-06 07:02:32,622 - INFO: Round 4: 21628749/21628749 AI 260817 AW 3500944
2022-05-06 07:04:37,665 - INFO: Round 5: 21628749/21628749 AI 261343 AW 3506372
2022-05-06 07:06:42,721 - INFO: Round 6: 21628749/21628749 AI 261761 AW 3510338
2022-05-06 07:08:47,729 - INFO: Round 7: 21628749/21628749 AI 262171 AW 3514592
2022-05-06 07:10:53,049 - INFO: Round 8: 21628749/21628749 AI 262471 AW 3517622
2022-05-06 07:12:57,915 - INFO: Round 9: 21628749/21628749 AI 262850 AW 3521528
2022-05-06 07:15:04,143 - INFO: Round 10: 21628749/21628749 AI 263231 AW 3525748
2022-05-06 07:17:12,231 - INFO: Round 11: 21628749/21628749 AI 263627 AW 3529660
2022-05-06 07:19:20,315 - INFO: Round 12: 21628749/21628749 AI 263966 AW 3533410
2022-05-06 07:21:25,894 - INFO: Round 13: 21628749/21628749 AI 264259 AW 3536486
2022-05-06 07:23:30,894 - INFO: Round 14: 21628749/21628749 AI 264570 AW 3539570
2022-05-06 07:25:35,770 - INFO: Round 15: 21628749/21628749 AI 264871 AW 3542922
2022-05-06 07:27:41,019 - INFO: Round 16: 21628749/21628749 AI 265147 AW 3545454
2022-05-06 07:29:46,536 - INFO: Round 17: 21628749/21628749 AI 265452 AW 3548476
2022-05-06 07:31:52,025 - INFO: Round 18: 21628749/21628749 AI 265728 AW 3551368
2022-05-06 07:33:57,677 - INFO: Round 19: 21628749/21628749 AI 266064 AW 3554624
2022-05-06 07:36:03,231 - INFO: Round 20: 21628749/21628749 AI 266474 AW 3558628
2022-05-06 07:38:08,600 - INFO: Round 21: 21628749/21628749 AI 266771 AW 3561496
2022-05-06 07:40:14,117 - INFO: Round 22: 21628749/21628749 AI 267022 AW 3563944
2022-05-06 07:42:19,171 - INFO: Round 23: 21628749/21628749 AI 267240 AW 3566100
2022-05-06 07:44:24,380 - INFO: Round 24: 21628749/21628749 AI 267438 AW 3568028
2022-05-06 07:46:29,766 - INFO: Round 25: 21628749/21628749 AI 267636 AW 3570060
2022-05-06 07:48:35,629 - INFO: Round 26: 21628749/21628749 AI 267878 AW 3572450
2022-05-06 07:50:41,145 - INFO: Round 27: 21628749/21628749 AI 268143 AW 3574974
2022-05-06 07:52:46,649 - INFO: Round 28: 21628749/21628749 AI 268346 AW 3577044
2022-05-06 07:54:51,972 - INFO: Round 29: 21628749/21628749 AI 268556 AW 3579282
2022-05-06 07:56:58,797 - INFO: Round 30: 21628749/21628749 AI 268768 AW 3581478
2022-05-06 07:59:06,195 - INFO: Round 31: 21628749/21628749 AI 268957 AW 3583424
2022-05-06 08:01:11,634 - INFO: Round 32: 21628749/21628749 AI 269165 AW 3585788
2022-05-06 08:03:17,434 - INFO: Round 33: 21628749/21628749 AI 269391 AW 3587926
2022-05-06 08:05:23,314 - INFO: Round 34: 21628749/21628749 AI 269634 AW 3590640
2022-05-06 08:07:28,951 - INFO: Round 35: 21628749/21628749 AI 269890 AW 3592876
2022-05-06 08:09:34,655 - INFO: Round 36: 21628749/21628749 AI 270089 AW 3594806
2022-05-06 08:11:39,762 - INFO: Round 37: 21628749/21628749 AI 270175 AW 3595712
2022-05-06 08:13:45,018 - INFO: Round 38: 21628749/21628749 AI 270302 AW 3597134
2022-05-06 08:15:50,368 - INFO: Round 39: 21628749/21628749 AI 270434 AW 3598488
2022-05-06 08:17:56,068 - INFO: Round 40: 21628749/21628749 AI 270550 AW 3599764
2022-05-06 08:20:01,391 - INFO: Round 41: 21628749/21628749 AI 270674 AW 3601230
2022-05-06 08:22:07,220 - INFO: Round 42: 21628749/21628749 AI 270798 AW 3602664
2022-05-06 08:24:12,601 - INFO: Round 43: 21628749/21628749 AI 270936 AW 3604094
2022-05-06 08:26:17,851 - INFO: Round 44: 21628749/21628749 AI 271097 AW 3605838
2022-05-06 08:28:23,200 - INFO: Round 45: 21628749/21628749 AI 271281 AW 3607854
2022-05-06 08:30:28,514 - INFO: Round 46: 21628749/21628749 AI 271502 AW 3609584
2022-05-06 08:32:33,553 - INFO: Round 47: 21628749/21628749 AI 271688 AW 3611862
2022-05-06 08:34:39,124 - INFO: Round 48: 21628749/21628749 AI 271849 AW 3613518
2022-05-06 08:36:44,400 - INFO: Round 49: 21628749/21628749 AI 272109 AW 3616548
2022-05-06 08:38:50,172 - INFO: Round 50: 21628749/21628749 AI 272334 AW 3619126
2022-05-06 08:38:50,172 - INFO: Hit the round limit 50 and terminated ...
2022-05-06 08:40:12,416 - INFO: Extending finished.

2022-05-06 08:40:13,373 - INFO: Separating extended fastq file ...
2022-05-06 08:40:15,563 - INFO: Setting '-k 21,45,65,85,105'
2022-05-06 08:40:15,563 - INFO: Assembling using SPAdes ...
2022-05-06 08:40:15,746 - INFO: spades.py -t 10 --phred-offset 33 -1 lh4_output/extended_1_paired.fq -2 lh4_output/extended_2_paired.fq --s1 lh4_output/extended_1_unpaired.fq --s2 lh4_output/extended_2_unpaired.fq -k 21,45,65,85,105 -o lh4_output/extended_spades
2022-05-06 08:41:42,376 - INFO: Insert size = 348.516, deviation = 66.9489, left quantile = 266, right quantile = 434
2022-05-06 08:41:42,376 - INFO: Assembling finished.

2022-05-06 08:41:49,640 - INFO: Slimming lh4_output/extended_spades/K105/assembly_graph.fastg finished!
2022-05-06 08:41:50,842 - INFO: Slimming lh4_output/extended_spades/K85/assembly_graph.fastg finished!
2022-05-06 08:41:52,039 - INFO: Slimming lh4_output/extended_spades/K65/assembly_graph.fastg finished!
2022-05-06 08:41:53,254 - INFO: Slimming lh4_output/extended_spades/K45/assembly_graph.fastg finished!
2022-05-06 08:41:53,254 - INFO: Slimming assembly graphs finished.

2022-05-06 08:41:53,254 - INFO: Extracting embplant_pt from the assemblies ...
2022-05-06 08:41:53,255 - INFO: Disentangling lh4_output/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-05-06 08:41:53,752 - INFO: Vertex_77304 #copy = 1
2022-05-06 08:41:53,752 - INFO: Vertex_77552_77610_77192 #copy = 1
2022-05-06 08:41:53,753 - INFO: Vertex_77604_77470_77492_77464 #copy = 2
2022-05-06 08:41:53,753 - INFO: Average embplant_pt kmer-coverage = 165.0
2022-05-06 08:41:53,753 - INFO: Average embplant_pt base-coverage = 538.1
2022-05-06 08:41:53,753 - INFO: Writing output ...
2022-05-06 08:41:53,811 - WARNING: More than one circular genome structure produced ...
2022-05-06 08:41:53,812 - WARNING: Please check the final result to confirm whether they are simply different in SSC direction (two flip-flop configurations)!
2022-05-06 08:41:54,389 - INFO: Detecting large repeats (>1000 bp) in PATH1 with IRs detected, Total:LSC:SSC:Repeat(bp) = 151257:82940:18389:24964
2022-05-06 08:41:54,389 - INFO: Writing PATH1 of complete embplant_pt to lh4_output/embplant_pt.K105.complete.graph1.1.path_sequence.fasta
2022-05-06 08:41:54,393 - INFO: Writing PATH2 of complete embplant_pt to lh4_output/embplant_pt.K105.complete.graph1.2.path_sequence.fasta
2022-05-06 08:41:54,393 - INFO: Writing GRAPH to lh4_output/embplant_pt.K105.complete.graph1.selected_graph.gfa
2022-05-06 08:41:54,475 - INFO: Result status of embplant_pt: circular genome
2022-05-06 08:41:54,540 - INFO: Please visualize lh4_output/extended_K105.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg using Bandage to confirm the final result.
2022-05-06 08:41:54,540 - INFO: Writing output finished.
2022-05-06 08:41:54,540 - INFO: Extracting embplant_pt from the assemblies finished.

Total cost 7400.14 s
Thank you!

Kinggerm · 2022-05-16T19:36:56Z

Kinggerm
May 16, 2022
Maintainer

The visualized *.fastg is mainly used for debugging, which means the data after "roughly filtering for target-like contigs" in the GetOrganelle paper Fig 1.
Please check it out https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02154-5/figures/1

The short answer is that everything is normal according to your log and graph files.

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Visualization of chloroplast genome assembly results #170

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Kinggerm May 16, 2022 Maintainer

wangyuhang970520
May 9, 2022

Kinggerm
May 16, 2022
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