GetOrganelle v1.7.6.1

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 3.8.13 (default, Mar 28 2022, 11:38:47)  [GCC 7.5.0]
PLATFORM: Linux mju-oceanpbi 4.18.0-373.el8.x86_64 #1 SMP Tue Mar 22 15:11:47 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.6.1; numpy 1.23.1; sympy 1.10.1; scipy 1.9.1
DEPENDENCIES: Blast 2.12.0
GETORG_PATH=/home/dahome/teachers/chenyanqiong/.GetOrganelle
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /home/dahome/teachers/chenyanqiong/project/cpAssemble/dapiaoX1
/home/dahome/teachers/chenyanqiong/miniconda3/envs/getorganelle/bin/get_organelle_from_assembly.py -g dapiao_6_spades/dapiao_output/assembly_graph.fastg -F embplant_pt -o dapiao_9 --min-depth 10

2022-12-30 09:04:40,173 - INFO: Processing assembly graph ...
2022-12-30 09:04:49,423 - INFO: Processing assembly graph finished.

2022-12-30 09:04:49,423 - INFO: Slimming assembly graph ...
2022-12-30 09:04:56,938 - INFO: Slimming dapiao_9/initial_assembly_graph.fastg finished!
2022-12-30 09:04:56,938 - INFO: Slimming assembly graph finished.

2022-12-30 09:04:56,939 - INFO: Extracting embplant_pt from the assemblies ...
2022-12-30 09:04:56,939 - INFO: Disentangling dapiao_9/slimmed_assembly_graph.fastg as a circular genome ... 
2022-12-30 09:04:57,067 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2022-12-30 09:04:57,067 - INFO: Disentangling dapiao_9/slimmed_assembly_graph.fastg as a circular genome ... 
2022-12-30 09:04:57,098 - INFO: Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
2022-12-30 09:04:57,098 - INFO: Disentangling dapiao_9/slimmed_assembly_graph.fastg as a/an embplant_pt-insufficient graph ... 
2022-12-30 09:04:57,834 - INFO: Average embplant_pt kmer-coverage = 139.4
2022-12-30 09:04:57,834 - INFO: Writing output ...
2022-12-30 09:04:57,917 - INFO: Writing PATH1 of embplant_pt scaffold(s) to dapiao_9/embplant_pt.scaffolds.graph1.1.path_sequence.fasta
2022-12-30 09:04:57,919 - INFO: Writing GRAPH to dapiao_9/embplant_pt.contigs.graph1.selected_graph.gfa
2022-12-30 09:04:57,920 - INFO: Result status of embplant_pt: 9 scaffold(s)
2022-12-30 09:04:57,920 - INFO: Writing output finished.
2022-12-30 09:04:57,920 - INFO: Please visualize dapiao_9/slimmed_assembly_graph.fastg and load dapiao_9/slimmed_assembly_graph.csv to confirm the incomplete result.
2022-12-30 09:04:57,920 - 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.
2022-12-30 09:04:57,920 - 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!
2022-12-30 09:04:57,920 - INFO: Extracting embplant_pt from the assemblies finished.


Total cost 27.10 s
Thank you!