2023-05-24 14:15:33,428 - INFO: Round 9: 10081574/10081574 AI 89119 AW 2714392 2023-05-24 14:15:33,428 - INFO: No more reads found and terminated ... 2023-05-24 14:16:02,153 - INFO: Extending finished.

[zlc952]

Dear Jianjun Jin,
Here is a question I would like to ask you.
I was running a sample in GO and got these messages:
2023-05-24 14:09:05,241 - INFO: Extending ...
2023-05-24 14:09:05,241 - INFO: Adding initial words ...
2023-05-24 14:09:10,357 - INFO: AW 2494456
2023-05-24 14:09:54,569 - INFO: Round 1: 10081574/10081574 AI 83350 AW 2659166
2023-05-24 14:10:37,037 - INFO: Round 2: 10081574/10081574 AI 86674 AW 2689496
2023-05-24 14:11:19,441 - INFO: Round 3: 10081574/10081574 AI 87740 AW 2700378
2023-05-24 14:12:01,859 - INFO: Round 4: 10081574/10081574 AI 88214 AW 2705138
2023-05-24 14:12:44,201 - INFO: Round 5: 10081574/10081574 AI 88789 AW 2711708
2023-05-24 14:13:26,559 - INFO: Round 6: 10081574/10081574 AI 89003 AW 2713300
2023-05-24 14:14:08,979 - INFO: Round 7: 10081574/10081574 AI 89101 AW 2714366
2023-05-24 14:14:51,291 - INFO: Round 8: 10081574/10081574 AI 89119 AW 2714392
2023-05-24 14:15:33,428 - INFO: Round 9: 10081574/10081574 AI 89119 AW 2714392
2023-05-24 14:15:33,428 - INFO: No more reads found and terminated ...
2023-05-24 14:16:02,153 - INFO: Extending finished.

2023-05-24 14:16:02,600 - INFO: Separating extended fastq file ...
2023-05-24 14:16:03,177 - INFO: Setting '-k 21,45,65,85,105'
2023-05-24 14:16:03,177 - INFO: Assembling using SPAdes ...
2023-05-24 14:16:03,218 - INFO: spades.py -t 1 --phred-offset 33 -1 plastome_output/extended_1_paired.fq -2 plastome_output/extended_2_paired.fq --s1 plastome_output/extended_1_unpaired.fq --s2 plastome_output/extended_2_unpaired.fq -k 21,45,65,85,105 -o plastome_output/extended_spades
2023-05-24 14:18:36,522 - INFO: Insert size = 249.129, deviation = 61.1604, left quantile = 178, right quantile = 329
2023-05-24 14:18:36,523 - INFO: Assembling finished.

2023-05-24 14:18:37,612 - INFO: Slimming plastome_output/extended_spades/K105/assembly_graph.fastg finished!
2023-05-24 14:18:38,480 - INFO: Slimming plastome_output/extended_spades/K85/assembly_graph.fastg finished!
2023-05-24 14:18:39,439 - INFO: Slimming plastome_output/extended_spades/K65/assembly_graph.fastg finished!
2023-05-24 14:18:40,361 - INFO: Slimming plastome_output/extended_spades/K45/assembly_graph.fastg finished!
2023-05-24 14:18:40,362 - INFO: Slimming assembly graphs finished.

2023-05-24 14:18:40,363 - INFO: Extracting embplant_pt from the assemblies ...
2023-05-24 14:18:40,364 - INFO: Disentangling plastome_output/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
^[[A^[[B

2023-05-24 14:48:40,364 - INFO: Disentangling timeout. (see '--disentangle-time-limit' for more)
2023-05-24 14:48:40,365 - INFO: Disentangling plastome_output/extended_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2023-05-24 15:18:40,365 - INFO: Disentangling timeout. (see '--disentangle-time-limit' for more)
2023-05-24 15:18:40,365 - INFO: Disentangling plastome_output/extended_spades/K65/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2023-05-24 15:18:40,730 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2023-05-24 15:18:40,730 - INFO: Disentangling plastome_output/extended_spades/K45/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2023-05-24 15:18:40,914 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_20758!'
2023-05-24 15:18:40,914 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ...
2023-05-24 15:18:40,914 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph.
2023-05-24 15:18:40,914 - INFO: Disentangling plastome_output/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2023-05-24 15:18:40,948 - WARNING: -100-bp gap/overlap between 72772 and 3550 indicated while conflicting connections existed!
2023-05-24 15:28:41,190 - INFO: Disentangling failed: 'Cannot identify copy number of 11016!'
2023-05-24 15:28:41,191 - INFO: Disentangling plastome_output/extended_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a/an embplant_pt-insufficient graph ...
2023-05-24 15:28:42,072 - WARNING: Self-loop contig detected: Vertex_3550_6574
2023-05-24 15:28:47,676 - INFO: Average embplant_pt kmer-coverage = 101.0
2023-05-24 15:28:47,676 - INFO: Average embplant_pt base-coverage = 335.3
2023-05-24 15:28:47,676 - INFO: Writing output ...
2023-05-24 15:28:47,719 - INFO: Writing PATH1 of embplant_pt scaffold(s) to plastome_output/embplant_pt.K105.scaffolds.graph1.1.path_sequence.fasta
2023-05-24 15:28:47,719 - INFO: Writing GRAPH to plastome_output/embplant_pt.K105.contigs.graph1.selected_graph.gfa
2023-05-24 15:28:47,720 - INFO: Result status of embplant_pt: 4 scaffold(s)
2023-05-24 15:28:47,840 - INFO: Writing output finished.
2023-05-24 15:28:47,841 - INFO: Please ...
2023-05-24 15:28:47,841 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg' in K105,K85,K65,K45
2023-05-24 15:28:47,841 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K105,K85,K65,K45
2023-05-24 15:28:47,841 - INFO: visualize and confirm the incomplete result in Bandage.
2023-05-24 15:28:47,842 - INFO: If the result is nearly complete,
2023-05-24 15:28:47,842 - 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
2023-05-24 15:28:47,842 - 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!
2023-05-24 15:28:47,842 - INFO: Extracting embplant_pt from the assemblies finished.

Thank you!

Thanks again for your help!

[JianjunJin]

• You need to follow the template for posting an issue and provide the complete log file!
• Questions MUST be posted in the Discussion!
• Please read the FAQ carefully before posting any questions.

[zlc952]

Hello! I am very sorry for not carefully reading the relevant rules before, which resulted in sending the wrong section.
Because the previous complete log file has been deleted, I ran the software package again, but the same problem still occurred.
Here is the complete log file. Could you please help me check the problem? Thank you very much!
get_org.log.txt