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 3.8.5 (default, Aug 25 2020, 08:59:16)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)]
PLATFORM: Linux r04n36 3.10.0-1062.4.1.el7.x86_64 #1 SMP Fri Oct 18 17:15:30 UTC 2019 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.6.1; numpy 1.23.5; sympy 1.11.1; scipy 1.9.3
DEPENDENCIES: Blast 2.9.0
GETORG_PATH=/home/54/bt305854/.GetOrganelle
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /scratch/bt305854/ApocynaceaeData/chloroplast/bbtools_assembly/V307/V307_spades/GetOrganelle_from_assembly_graph_with_scaffolds_V307
/home/54/bt305854/GetOrganelle_venv/GetOrganelle/get_organelle_from_assembly.py -g slimmed_assembly_graph_no_189444.gfa -F embplant_pt -o GetOrganelle_from_assembly_graph_with_scaffolds_V307 -t 2

2022-12-22 12:13:53,035 - INFO: Processing assembly graph ...
2022-12-22 12:13:53,208 - INFO: Processing assembly graph finished.

2022-12-22 12:13:53,208 - INFO: Slimming assembly graph ...
2022-12-22 12:13:56,105 - INFO: Slimming GetOrganelle_from_assembly_graph_with_scaffolds_V307/initial_assembly_graph.gfa finished!
2022-12-22 12:13:56,106 - INFO: Slimming assembly graph finished.

2022-12-22 12:13:56,106 - INFO: Extracting embplant_pt from the assemblies ...
2022-12-22 12:13:56,107 - INFO: Disentangling GetOrganelle_from_assembly_graph_with_scaffolds_V307/slimmed_assembly_graph.gfa as a circular genome ... 
2022-12-22 12:13:56,191 - INFO: Consensus made: (187292-|189390+)
2022-12-22 12:13:56,192 - WARNING: The graph might suffer from contamination or polymorphism!
2022-12-22 12:13:57,746 - INFO: Vertex_186851_189490_188784 #copy = 1
2022-12-22 12:13:57,746 - INFO: Vertex_187740 #copy = 2
2022-12-22 12:13:57,746 - INFO: Vertex_187742 #copy = 4
2022-12-22 12:13:57,746 - INFO: Vertex_188912 #copy = 2
2022-12-22 12:13:57,746 - INFO: Vertex_189492_184015_188832_188940_189360_168993_185021_188802_189480_189426_(187292-|189390+)_189488_189458_189454_189484 #copy = 1
2022-12-22 12:13:57,746 - INFO: Vertex_189494_188676 #copy = 2
2022-12-22 12:13:57,746 - INFO: Average embplant_pt kmer-coverage = 169.5
2022-12-22 12:13:57,746 - INFO: Writing output ...
2022-12-22 12:13:57,825 - WARNING: Multiple repeat patterns appeared in your data, a more balanced pattern (always the repeat_pattern1) would be suggested for plastomes with the canonical IR!
2022-12-22 12:13:57,825 - WARNING: Multiple circular genome structures produced!
2022-12-22 12:13:57,825 - WARNING: Please check the existence of those isomers by using reads mapping (library information) or longer reads.
2022-12-22 12:13:57,954 - INFO: Writing PATH1 of nearly-complete embplant_pt to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.1.repeat_pattern1.path_sequence.fasta
2022-12-22 12:13:58,041 - INFO: Writing PATH2 of nearly-complete embplant_pt to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.2.repeat_pattern1.path_sequence.fasta
2022-12-22 12:13:58,067 - INFO: Writing PATH3 of nearly-complete embplant_pt to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.3.repeat_pattern2.path_sequence.fasta
2022-12-22 12:13:58,086 - INFO: Writing PATH4 of nearly-complete embplant_pt to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.4.repeat_pattern2.path_sequence.fasta
2022-12-22 12:13:58,149 - INFO: Writing PATH5 of nearly-complete embplant_pt to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.5.repeat_pattern2.path_sequence.fasta
2022-12-22 12:13:58,163 - INFO: Writing PATH6 of nearly-complete embplant_pt to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.6.repeat_pattern2.path_sequence.fasta
2022-12-22 12:13:58,163 - INFO: Writing GRAPH to GetOrganelle_from_assembly_graph_with_scaffolds_V307/embplant_pt.nearly-complete.graph1.selected_graph.gfa
2022-12-22 12:13:58,250 - INFO: Result status of embplant_pt: circular genome with gaps
2022-12-22 12:13:58,251 - WARNING: Degenerate base(s) used!
2022-12-22 12:13:58,251 - INFO: Please visualize GetOrganelle_from_assembly_graph_with_scaffolds_V307/slimmed_assembly_graph.gfa and load GetOrganelle_from_assembly_graph_with_scaffolds_V307/slimmed_assembly_graph.csv using Bandage to confirm the final result.
2022-12-22 12:13:58,251 - INFO: Writing output finished.
2022-12-22 12:13:58,251 - INFO: Extracting embplant_pt from the assemblies finished.


Total cost 232.73 s
Thank you!