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Incomplete animal mitochondria #306

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mahziar121 opened this issue Jan 4, 2024 · 11 comments
Closed
3 tasks done

Incomplete animal mitochondria #306

mahziar121 opened this issue Jan 4, 2024 · 11 comments

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@mahziar121
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mahziar121 commented Jan 4, 2024 •
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Hello,

I want to assemble the mitogenome of a wasp. I used three related complete mitogenomes as a seed. I get a 14829 bp linear scaffold but not a circular mitogenome. How can get the complete genome. Please see my script and GFA file below:

#!/bin/bash -l
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=900GB
#SBATCH --time=14-00:00:00
#SBATCH --mail-user=[email protected]
#SBATCH --mail-type=ALL
#SBATCH --job-name="GetOrganelle-Wasp-Mitochondria-Assembly27"
#SBATCH -p highmem

module load getorganelle/1.7.6

get_organelle_from_reads.py -s "/rhome/mkhaz002/3completemitogenome.fasta" -1 "/bigdata/adamslab/mkhaz002/WholeGenomSequence/TrimmedwithTrimmomatic/WA_lib_051823_S1_L002_R1_001_paired_trimmed.fastq.gz" -2 "/bigdata/adamslab/mkhaz002/WholeGenomSequence/TrimmedwithTrimmomatic/WA_lib_051823_S1_L002_R2_001_paired_trimmed.fastq.gz" -k 21,27,33,41,45,51,55,65,75,85,91,95,101,105,111,115,121,127 -F animal_mt -o "/bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle27/" -R 40 --overwrite -t 32 --reduce-reads-for-coverage inf --max-reads inf --max-extending-len inf --disentangle-time-limit 1080000

get_org.log.txt

image image

First check

  • I used the GitHub search to find a similar issue or discussion and didn't find it.
  • I searched GetOrganelle.wiki context, especially the FAQ and browsed the examples to confirm it is unexpected to happen.
  • I have updated GetOrganelle to the latest released version GitHub release

Please ask questions in the Question in GitHub Discussions unless it is a feature request or bug report.
@JianjunJin
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Thank you for your post and for using GetOrganelle. I noticed your message, and I appreciate the effort you've made to detail your process.

However, I must mention that the GetOrganelle version in your log appears to be outdated, contrary to the claim of being the latest version. This is crucial for effective troubleshooting. While I understand your frustration, it’s essential to ensure that we are working with the most updated version of GetOrganelle for accurate support.

Additionally, addressing the pending concern in issue #299 would greatly assist in providing comprehensive help.

I encourage you to update GetOrganelle to the latest version and revisit issue #299. Once these steps are taken, I'll be more than willing to offer further assistance in improving your assembly results.

@mahziar121
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get_org.log.txt
Could you please take a look at the log? Firstly, there was only one extension round. Secondly, the analysis is taking a lot of time, maybe due to the disentangle-time-limit parameter set to 1080000. It has been more than 15 days and the analysis is still in the slimming phase. Do you have any suggestions to improve my analysis?

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 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0]
PLATFORM: Linux h01 4.18.0-477.21.1.el8_8.x86_64 #1 SMP Tue Aug 8 21:30:09 UTC 2023 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.21.6; sympy 1.10.1; scipy 1.7.3
DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.12.0
GETORG_PATH=/rhome/mkhaz002/.GetOrganelle
LABEL DB: animal_mt 0.0.1
WORKING DIR: /rhome/mkhaz002
/opt/linux/rocky/8.x/x86_64/pkgs/getorganelle/1.7.7.0/bin/get_organelle_from_reads.py -s /rhome/mkhaz002/3completemitogenome.fasta -1 /bigdata/adamslab/mkhaz002/WholeGenomSequence/TrimmedwithTrimmomatic/WA_lib_051823_S1_L002_R1_001_paired_trimmed.fastq.gz -2 /bigdata/adamslab/mkhaz002/WholeGenomSequence/TrimmedwithTrimmomatic/WA_lib_051823_S1_L002_R2_001_paired_trimmed.fastq.gz -k 21,27,33,41,45,51,55,65,75,85,91,95,101,105,111,115,121,125,127 -F animal_mt -o /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/ -R 40 --overwrite -t 32 --reduce-reads-for-coverage inf --max-reads inf --max-extending-len inf --disentangle-time-limit 1080000 -w 65

2024-01-04 15:02:06,387 - INFO: Pre-reading fastq ...
2024-01-04 15:02:06,387 - INFO: Unzipping reads file: /bigdata/adamslab/mkhaz002/WholeGenomSequence/TrimmedwithTrimmomatic/WA_lib_051823_S1_L002_R1_001_paired_trimmed.fastq.gz (14060107484 bytes)
2024-01-04 15:10:05,975 - INFO: Unzipping reads file: /bigdata/adamslab/mkhaz002/WholeGenomSequence/TrimmedwithTrimmomatic/WA_lib_051823_S1_L002_R2_001_paired_trimmed.fastq.gz (14687636100 bytes)
2024-01-04 15:18:16,667 - INFO: Counting read qualities ...
2024-01-04 15:18:17,040 - INFO: Identified quality encoding format = Sanger
2024-01-04 15:18:17,041 - INFO: Phred offset = 33
2024-01-04 15:18:17,042 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2024-01-04 15:18:17,084 - INFO: Mean error rate = 0.0022
2024-01-04 15:18:17,085 - INFO: Counting read lengths ...
2024-01-04 15:32:49,557 - INFO: Mean = 146.6 bp, maximum = 150 bp.
2024-01-04 15:32:49,558 - INFO: Reads used = 225798090+225798090
2024-01-04 15:32:49,558 - INFO: Pre-reading fastq finished.

2024-01-04 15:32:49,558 - INFO: Making seed reads ...
2024-01-04 15:32:49,682 - INFO: Making seed - bowtie2 index ...
2024-01-04 15:32:50,266 - INFO: Making seed - bowtie2 index finished.
2024-01-04 15:32:50,267 - INFO: Mapping reads to seed bowtie2 index ...
2024-01-04 16:45:04,608 - INFO: Mapping finished.
2024-01-04 16:45:04,609 - INFO: Seed reads made: /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/seed/animal_mt.initial.fq (137052 bytes)
2024-01-04 16:45:04,635 - INFO: Making seed reads finished.

2024-01-04 16:45:04,635 - INFO: Checking seed reads and parameters ...
2024-01-04 16:45:05,118 - INFO: Estimated animal_mt-hitting base-coverage = 278.05
2024-01-04 16:45:05,955 - INFO: Setting '--max-extending-len inf'
2024-01-04 16:45:05,956 - INFO: Checking seed reads and parameters finished.

2024-01-04 16:45:05,956 - INFO: Making read index ...
2024-01-04 18:33:04,680 - INFO: 357522123 candidates in all 451596180 reads
2024-01-04 18:33:04,684 - INFO: Pre-grouping reads ...
2024-01-04 18:33:04,684 - INFO: Setting '--pre-w 65'
2024-01-04 18:33:45,433 - INFO: 200000/59131022 used/duplicated
2024-01-04 18:34:25,594 - INFO: 5185 groups made.
2024-01-04 18:36:41,295 - INFO: Making read index finished.

2024-01-04 18:36:41,300 - INFO: Extending ...
2024-01-04 18:36:41,300 - INFO: Adding initial words ...
2024-01-04 18:36:41,332 - INFO: AW 3246
2024-01-04 18:57:25,309 - INFO: Round 1: 66141571/357522123 AI 19996065 AW 200067830
2024-01-04 18:57:25,313 - INFO: Hit the words limit and terminated ...
2024-01-04 18:57:25,313 - WARNING: Terminated at an insufficient number of rounds, see '--max-n-words'/'--max-extending-len' for more.
2024-01-04 19:24:58,794 - INFO: Extending finished.

2024-01-04 19:24:58,824 - INFO: Separating extended fastq file ...
2024-01-04 19:26:54,516 - WARNING: No paired reads found?!
2024-01-04 19:26:54,537 - INFO: Setting '-k 21,27,33,41,45,51,55,65,75,85,91,95,101,105,111,115,121,125,127'
2024-01-04 19:26:54,537 - INFO: Assembling using SPAdes ...
2024-01-04 19:26:54,587 - INFO: spades.py -t 32 --phred-offset 33 --s1 /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_1_unpaired.fq -k 21,27,33,41,45,51,55,65,75,85,91,95,101,105,111,115,121,125,127 -o /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades
2024-01-05 00:24:27,010 - INFO: Assembling finished.

2024-01-05 00:32:25,485 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K127/assembly_graph.fastg finished!
2024-01-05 00:46:04,733 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K125/assembly_graph.fastg finished!
2024-01-05 12:34:48,210 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K121/assembly_graph.fastg finished!
2024-01-06 05:26:05,086 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K115/assembly_graph.fastg finished!
2024-01-07 05:23:24,453 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K111/assembly_graph.fastg finished!
2024-01-08 13:53:30,813 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K105/assembly_graph.fastg finished!
2024-01-10 04:31:26,291 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K101/assembly_graph.fastg finished!
2024-01-12 10:37:19,707 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K95/assembly_graph.fastg finished!
2024-01-14 22:23:56,540 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K91/assembly_graph.fastg finished!
2024-01-17 20:22:42,774 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle29/extended_spades/K85/assembly_graph.fastg finished!

@mahziar121
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mahziar121 commented Jan 20, 2024 via email

@JianjunJin
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Dear mahziar,

Thank you for updating GetOrganelle to the latest version as per current issue. However, I must express my concern regarding issue #299 . It is crucial to maintain good practice by addressing open issues, which ensures effective communication and resolution of problems.

Regarding your assembly challenge:

  1. The graph is insufficient due to a small word size (-w). This limitation is more pronounced in datasets with large and complex samples. I suggest increasing the word size to potentially achieve a more comprehensive graph. Note that your recent updates with smaller word sizes were counterproductive to this goal.
  2. Many repeats were observed (probably around the D-loop), potentially creating challenges even when you get a sufficient graph later.

I will close issue #299 due to lack of progress. Please keep these guidelines in mind for future interactions. Your adherence to proper issue handling is appreciated and will ensure more efficient support.

@mahziar121
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Hello, I got a circular genome, but I don't know how to finalize it using BANDAGE.

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 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0]
PLATFORM: Linux h03 4.18.0-477.21.1.el8_8.x86_64 #1 SMP Tue Aug 8 21:30:09 UTC 2023 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.21.6; sympy 1.10.1; scipy 1.7.3
DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.12.0
GETORG_PATH=/rhome/mkhaz002/.GetOrganelle
LABEL DB: animal_mt 0.0.1
WORKING DIR: /rhome/mkhaz002
/opt/linux/rocky/8.x/x86_64/pkgs/getorganelle/1.7.7.0/bin/get_organelle_from_reads.py -s /rhome/mkhaz002/3completemitogenome.fasta -1 /bigdata/adamslab/mkhaz002/Genomic_raw_reads_from_Ampulex_compressa/SRR14607679-8000/SRR14607679_pass_1.fastq -2 /bigdata/adamslab/mkhaz002/Genomic_raw_reads_from_Ampulex_compressa/SRR14607679-8000/SRR14607679_pass_2.fastq -k 21,55,85,105,115,127 -F animal_mt -o /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/ -R 40 --overwrite -t 32 --reduce-reads-for-coverage inf --max-reads inf --max-extending-len inf --disentangle-time-limit 1080000 -w 127

2024-01-27 15:34:50,367 - INFO: Pre-reading fastq ...
2024-01-27 15:36:21,154 - INFO: Counting read qualities ...
2024-01-27 15:36:21,323 - INFO: Identified quality encoding format = Illumina 1.8+
2024-01-27 15:36:21,323 - INFO: Phred offset = 33
2024-01-27 15:36:21,324 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2024-01-27 15:36:21,434 - INFO: Mean error rate = 0.0164
2024-01-27 15:36:21,435 - INFO: Counting read lengths ...
2024-01-27 15:43:59,414 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2024-01-27 15:43:59,418 - INFO: Reads used = 117082903+117082903
2024-01-27 15:43:59,418 - INFO: Pre-reading fastq finished.

2024-01-27 15:43:59,418 - INFO: Making seed reads ...
2024-01-27 15:43:59,452 - INFO: Making seed - bowtie2 index ...
2024-01-27 15:43:59,984 - INFO: Making seed - bowtie2 index finished.
2024-01-27 15:43:59,985 - INFO: Mapping reads to seed bowtie2 index ...
2024-01-27 16:22:04,658 - INFO: Mapping finished.
2024-01-27 16:22:04,662 - INFO: Seed reads made: /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/seed/animal_mt.initial.fq (209108 bytes)
2024-01-27 16:22:04,663 - INFO: Making seed reads finished.

2024-01-27 16:22:04,663 - INFO: Checking seed reads and parameters ...
2024-01-27 16:22:05,119 - INFO: Estimated animal_mt-hitting base-coverage = 270.00
2024-01-27 16:22:05,827 - INFO: Setting '--max-extending-len inf'
2024-01-27 16:22:05,829 - INFO: Checking seed reads and parameters finished.

2024-01-27 16:22:05,829 - INFO: Making read index ...
2024-01-27 17:12:40,551 - INFO: 218530812 candidates in all 234165806 reads
2024-01-27 17:12:40,554 - INFO: Pre-grouping reads ...
2024-01-27 17:12:40,555 - INFO: Setting '--pre-w 127'
2024-01-27 17:13:02,965 - INFO: 200000/7077664 used/duplicated
2024-01-27 17:13:21,879 - INFO: 5987 groups made.
2024-01-27 17:14:24,004 - INFO: Making read index finished.

2024-01-27 17:14:24,004 - INFO: Extending ...
2024-01-27 17:14:24,004 - INFO: Adding initial words ...
2024-01-27 17:14:24,030 - INFO: AW 6686
2024-01-27 17:29:23,064 - INFO: Round 1: 218530812/218530812 AI 94008 AW 90170
2024-01-27 17:44:30,385 - INFO: Round 2: 218530812/218530812 AI 160880 AW 162086
2024-01-27 17:59:23,421 - INFO: Round 3: 218530812/218530812 AI 201626 AW 198198
2024-01-27 18:14:19,751 - INFO: Round 4: 218530812/218530812 AI 208281 AW 204598
2024-01-27 18:29:18,576 - INFO: Round 5: 218530812/218530812 AI 208415 AW 205554
2024-01-27 18:44:15,013 - INFO: Round 6: 218530812/218530812 AI 208517 AW 205864
2024-01-27 18:59:12,347 - INFO: Round 7: 218530812/218530812 AI 208595 AW 206162
2024-01-27 19:14:10,393 - INFO: Round 8: 218530812/218530812 AI 208699 AW 206528
2024-01-27 19:29:09,037 - INFO: Round 9: 218530812/218530812 AI 208745 AW 206684
2024-01-27 19:44:08,269 - INFO: Round 10: 218530812/218530812 AI 208814 AW 207124
2024-01-27 19:59:04,637 - INFO: Round 11: 218530812/218530812 AI 208924 AW 207476
2024-01-27 20:14:00,507 - INFO: Round 12: 218530812/218530812 AI 209029 AW 207800
2024-01-27 20:28:58,217 - INFO: Round 13: 218530812/218530812 AI 209178 AW 208294
2024-01-27 20:43:58,304 - INFO: Round 14: 218530812/218530812 AI 209313 AW 208690
2024-01-27 20:58:58,193 - INFO: Round 15: 218530812/218530812 AI 209441 AW 209180
2024-01-27 21:13:56,939 - INFO: Round 16: 218530812/218530812 AI 209549 AW 209498
2024-01-27 21:28:54,778 - INFO: Round 17: 218530812/218530812 AI 209615 AW 209744
2024-01-27 21:43:52,826 - INFO: Round 18: 218530812/218530812 AI 209711 AW 210138
2024-01-27 21:58:52,476 - INFO: Round 19: 218530812/218530812 AI 209822 AW 210476
2024-01-27 22:13:49,847 - INFO: Round 20: 218530812/218530812 AI 209884 AW 210780
2024-01-27 22:28:49,356 - INFO: Round 21: 218530812/218530812 AI 209960 AW 211226
2024-01-27 22:43:49,653 - INFO: Round 22: 218530812/218530812 AI 210138 AW 212088
2024-01-27 22:58:51,920 - INFO: Round 23: 218530812/218530812 AI 210272 AW 212638
2024-01-27 23:13:52,225 - INFO: Round 24: 218530812/218530812 AI 210396 AW 213298
2024-01-27 23:28:53,977 - INFO: Round 25: 218530812/218530812 AI 210645 AW 214382
2024-01-27 23:43:53,081 - INFO: Round 26: 218530812/218530812 AI 210827 AW 215142
2024-01-27 23:58:58,180 - INFO: Round 27: 218530812/218530812 AI 210996 AW 215850
2024-01-28 00:14:20,766 - INFO: Round 28: 218530812/218530812 AI 211192 AW 216660
2024-01-28 00:29:28,005 - INFO: Round 29: 218530812/218530812 AI 211358 AW 217516
2024-01-28 00:44:32,015 - INFO: Round 30: 218530812/218530812 AI 211529 AW 218142
2024-01-28 00:59:35,740 - INFO: Round 31: 218530812/218530812 AI 211737 AW 218950
2024-01-28 01:14:37,370 - INFO: Round 32: 218530812/218530812 AI 212002 AW 220850
2024-01-28 01:30:02,804 - INFO: Round 33: 218530812/218530812 AI 266520 AW 481286
2024-01-28 01:46:00,398 - INFO: Round 34: 218530812/218530812 AI 362488 AW 891164
2024-01-28 02:03:19,344 - INFO: Round 35: 218530812/218530812 AI 3688159 AW 19726828
2024-01-28 02:25:08,430 - INFO: Round 36: 218530812/218530812 AI 28104873 AW 98025966
2024-01-28 02:43:11,272 - INFO: Round 37: 218530812/218530812 AI 37680918 AW 132069034
2024-01-28 03:00:04,557 - INFO: Round 38: 218530812/218530812 AI 41419204 AW 143853210
2024-01-28 03:16:50,591 - INFO: Round 39: 218530812/218530812 AI 44821887 AW 161226446
2024-01-28 03:32:21,865 - INFO: Round 40: 218530812/218530812 AI 46093402 AW 166254652
2024-01-28 03:32:21,972 - INFO: Hit the round limit 40 and terminated ...
2024-01-28 03:57:25,998 - INFO: Extending finished.

2024-01-28 03:57:26,118 - INFO: Separating extended fastq file ...
2024-01-28 04:03:03,446 - INFO: Setting '-k 21,55,85,105,115,127'
2024-01-28 04:03:03,454 - INFO: Assembling using SPAdes ...
2024-01-28 04:03:03,531 - INFO: spades.py -t 32 --phred-offset 33 -1 /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_1_paired.fq -2 /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_2_paired.fq --s1 /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_1_unpaired.fq --s2 /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_2_unpaired.fq -k 21,55,85,105,115,127 -o /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades
2024-01-28 06:51:18,298 - INFO: Insert size = 232.109, deviation = 20.1651, left quantile = 205, right quantile = 254
2024-01-28 06:51:18,325 - INFO: Assembling finished.

2024-01-28 07:02:32,386 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K127/assembly_graph.fastg finished!
2024-01-28 13:30:41,433 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K115/assembly_graph.fastg finished!
2024-01-28 19:50:56,450 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K105/assembly_graph.fastg finished!
2024-01-29 07:55:17,026 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K85/assembly_graph.fastg finished!
2024-01-29 15:12:21,061 - INFO: Slimming /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K55/assembly_graph.fastg finished!
2024-01-29 15:12:21,083 - INFO: Slimming assembly graphs finished.

2024-01-29 15:12:21,083 - INFO: Extracting animal_mt from the assemblies ...
2024-01-29 15:12:21,360 - INFO: Disentangling /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K127/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2024-01-29 15:12:26,028 - WARNING: Self-loop contig detected: Vertex_41778578_38608484
2024-01-29 15:13:36,336 - INFO: Disentangling failed: 'Incomplete/Complicated/Unsolvable target graph (3)!'
2024-01-29 15:13:36,337 - INFO: Disentangling /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K115/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2024-01-29 15:13:40,164 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_51408196!'
2024-01-29 15:13:40,165 - INFO: Disentangling /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_spades/K105/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ...
2024-01-29 17:50:10,732 - WARNING: The graph might suffer from contamination or polymorphism!
2024-01-29 17:50:10,736 - WARNING: Only the contig with the max cov was kept for each of those 1 polymorphic loci.
2024-01-29 17:50:10,778 - INFO: Vertex_36548606_889808 #copy = 1
2024-01-29 17:50:10,779 - INFO: Vertex_37750020_37106146_48652240 #copy = 2
2024-01-29 17:50:10,779 - INFO: Vertex_41927594_48323408_35234416_41231834_44654302_36939412_48652242_47465100_48653854_48672056 #copy = 1
2024-01-29 17:50:10,779 - INFO: Average animal_mt kmer-coverage = 925.5
2024-01-29 17:50:10,779 - INFO: Average animal_mt base-coverage = 3017.9
2024-01-29 17:50:10,783 - INFO: Writing output ...
2024-01-29 17:50:10,800 - INFO: Writing PATH1 of complete animal_mt to /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/animal_mt.K105.complete.graph1.1.path_sequence.fasta
2024-01-29 17:50:10,810 - INFO: Writing GRAPH to /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/animal_mt.K105.complete.graph1.selected_graph.gfa
2024-01-29 17:50:10,833 - INFO: Result status of animal_mt: circular genome
2024-01-29 17:50:11,350 - INFO: Please visualize /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/extended_K105.assembly_graph.fastg.extend-animal_mt.fastg using Bandage to confirm the final result.
2024-01-29 17:50:11,350 - INFO: Writing output finished.
2024-01-29 17:50:13,399 - INFO: Extracting animal_mt from the assemblies finished.

Total cost 180928.34 s
Thank you!
extended_K105.assembly_graph.fastg.extend-animal_mt.csv
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mahziar121 commented Jan 30, 2024 via email

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JianjunJin commented Jan 30, 2024 •
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Congrats on the success after parameter finetuning!

You don't need to do it yourself in Bandage, which is mainly for checking.
As mentioned in the log file, the final result is available at /bigdata/adamslab/mkhaz002/WholeGenomSequence/GetOrganelle43/animal_mt.K105.complete.graph1.1.path_sequence.fasta.

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mahziar121 commented Jan 30, 2024 via email

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mahziar121 commented Jan 30, 2024 via email

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Circular topology is just an attribute of a sequence. In a fasta file, a circular sequence is no different from a linear one at the bases.

People usually put annotations in the header to denote the sequence as circular. However, different tools recognize the circular notation in different ways. GetOrganelle follows the Bandage notation, (circular). It doesn't matter how snapgene and Geneious recognize it; at least in Geneious, you can manually set the sequence to be circular.

The file cannot be attached via email. Next time, please change the postfix of the file into txt and manually attach it via the GitHub portal. But I don't need it this time.

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mahziar121 commented Jan 30, 2024 via email

Repository owner locked and limited conversation to collaborators Apr 3, 2024
@JianjunJin JianjunJin converted this issue into discussion #325 Apr 3, 2024

This issue was moved to a discussion.

You can continue the conversation there. Go to discussion →

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