How can I resolve the problem: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?

[lychen83]

Hi Dr Jin,

I am using GetOrganelle for assemble my cp. I have 25 Gb pair-end NGS data (150bp * 2).
When I assembled it, I confronted a warning:
'2021-07-27 16:45:10,295 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?''
The software failed to get a complete cp genome.

I also have the long reads, HIFI. I assembled them using hiasm. Then use the *p_utg.gfa as input for GetOrganelle. However, I confronted the same warning.

Could you kindly give any suggestions?

Thank you.

Best,
Lingyun

The log is as following:
<[lyc@248 ZLH]$ get_organelle_from_assembly.py -F embplant_pt -g zlh_m6416_hifi_reads.asm.bp.p_utg.gfa -o ZLH_pt_hiasm_get_organelle --overwrite

GetOrganelle v1.7.5

get_organelle_from_assembly.py isolates organelle genomes from assembly graph.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.4 (default, Aug 13 2019, 20:35:49) [GCC 7.3.0]
PLATFORM: Linux 248.189.119.202.cpu.edu.cn.189.119.202.in-addr.arpa 4.18.0-240.1.1.el8_3.x86_64 #1 SMP Thu Nov 19 17:20:08 UTC 2020 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.5; numpy 1.17.2; sympy 1.4; scipy 1.3.1
DEPENDENCIES: Blast 2.9.0; Bandage 0.8.1
GETORG_PATH=/home/lyc/.GetOrganelle
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /home/lyc/data/shuying/cp_mt/ZLH
/home/lyc/software/Anaconda3-2019.10_installed_dec2020/bin/get_organelle_from_assembly.py -F embplant_pt -g zlh_m6416_hifi_reads.asm.bp.p_utg.gfa -o ZLH_pt_hiasm_get_organelle --overwrite

2021-07-27 21:08:57,275 - INFO: Processing assembly graph ...
2021-07-27 21:08:57,665 - INFO: Processing assembly graph finished.

2021-07-27 21:08:57,666 - INFO: Slimming assembly graph ...
2021-07-27 21:11:08,877 - INFO: Slimming ZLH_pt_hiasm_get_organelle/initial_assembly_graph.gfa finished!
2021-07-27 21:11:08,877 - INFO: Slimming assembly graph finished.

2021-07-27 21:11:08,877 - INFO: Extracting embplant_pt from the assemblies ...
2021-07-27 21:11:08,878 - INFO: Disentangling ZLH_pt_hiasm_get_organelle/slimmed_assembly_graph.gfa as a circular genome ...
/home/lyc/software/Anaconda3-2019.10_installed_dec2020/lib/python3.7/site-packages/GetOrganelleLib/../numpy/lib/scimath.py:274: RuntimeWarning: divide by zero encountered in log
return nx.log(x)
2021-07-27 21:11:10,134 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2021-07-27 21:11:10,136 - INFO: Disentangling ZLH_pt_hiasm_get_organelle/slimmed_assembly_graph.gfa as a circular genome ...
2021-07-27 21:11:11,165 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2021-07-27 21:11:11,168 - INFO: Disentangling ZLH_pt_hiasm_get_organelle/slimmed_assembly_graph.gfa as a/an embplant_pt-insufficient graph ...
2021-07-27 21:11:12,429 - INFO: Average embplant_pt coverage = 37.2
2021-07-27 21:11:12,429 - INFO: Writing output ...
2021-07-27 21:11:35,296 - INFO: Writing PATH1 of embplant_pt scaffold(s) to ZLH_pt_hiasm_get_organelle/embplant_pt.scaffolds.graph1.1.path_sequence.fasta
2021-07-27 21:11:35,348 - INFO: Writing GRAPH to ZLH_pt_hiasm_get_organelle/embplant_pt.contigs.graph1.selected_graph.gfa
2021-07-27 21:11:35,379 - INFO: Result status of embplant_pt: 20 scaffold(s)
2021-07-27 21:11:35,379 - INFO: Writing output finished.
2021-07-27 21:11:35,382 - INFO: Please visualize ZLH_pt_hiasm_get_organelle/slimmed_assembly_graph.gfa and load ZLH_pt_hiasm_get_organelle/slimmed_assembly_graph.csv to confirm the incomplete result.
2021-07-27 21:11:35,382 - INFO: If the result is nearly complete, you can try join_spades_fastg_by_blast.py to fill N-gaps in-between contigs with a closely-related reference.
2021-07-27 21:11:35,382 - 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!
2021-07-27 21:11:35,382 - INFO: Extracting embplant_pt from the assemblies finished.

Total cost 159.31 s
Thank you!>

[Kinggerm]

Please always attach the complete log file and the post-slimming graph as the log already indicated.

[lychen83]

lingyun.zip

Thanks,

The log file and the graph file were attached.
I appreciate your help.

Lingyun

[d8a23f]

Hi, Dear lychen83
I have the same problem, have you solved it.
INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_2531!'

[Kinggerm]

lingyun.zip

Thanks,

The log file and the graph file were attached.
I appreciate your help.

Lingyun

For the NGS result you attached, please refer to FAQ first.
https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#what-should-i-do-with-incomplete-resultbroken-assembly-graph
This is an organelle insufficient graph and please rerun GetOrganelle with parameters adjusted accordingly.

[d8a23f]

lingyun.zip
Thanks,
The log file and the graph file were attached.
I appreciate your help.
Lingyun

For the NGS result you attached, please refer to FAQ first.
https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#what-should-i-do-with-incomplete-resultbroken-assembly-graph
This is an organelle insufficient graph and please rerun GetOrganelle with parameters adjusted accordingily.

thanks a lot, I will try

[Rebecca-zhou-sm]

Hello, I also had the same problem, please how did you solve it, thank you @lychen83