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 5CG8284Z7V 5.10.102.1-microsoft-standard-WSL2 #1 SMP Wed Mar 2 00:30:59 UTC 2022 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 3.15.4; Blast 2.12.0
GETORG_PATH=/home/snrnp/.GetOrganelle
LABEL DB: animal_mt 0.0.1
WORKING DIR: /mnt/c/GeneticsData/Bneb_getorg
/home/snrnp/miniconda3/envs/getorganelle/bin/get_organelle_from_reads.py -1 pair1.fastq -2 pair2.fastq -s Bgabbii.fasta --reduce-reads-for-coverage inf -R 10 -k 21,45,65,85,105 -F animal_mt -o get_org_3

2023-08-09 09:58:51,998 - INFO: Pre-reading fastq ...
2023-08-09 10:00:00,049 - INFO: Counting read qualities ...
2023-08-09 10:00:00,452 - INFO: Identified quality encoding format = Sanger
2023-08-09 10:00:00,452 - INFO: Phred offset = 33
2023-08-09 10:00:00,454 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2023-08-09 10:00:00,496 - INFO: Mean error rate = 0.001
2023-08-09 10:00:00,498 - INFO: Counting read lengths ...
2023-08-09 10:00:17,730 - INFO: Mean = 142.4 bp, maximum = 143 bp.
2023-08-09 10:00:17,735 - INFO: Reads used = 561392+561392
2023-08-09 10:00:17,736 - INFO: Pre-reading fastq finished.

2023-08-09 10:00:17,737 - INFO: Making seed reads ...
2023-08-09 10:00:17,793 - INFO: Making seed - bowtie2 index ...
2023-08-09 10:00:18,839 - INFO: Making seed - bowtie2 index finished.
2023-08-09 10:00:18,840 - INFO: Mapping reads to seed bowtie2 index ...
2023-08-09 10:02:07,014 - INFO: Mapping finished.
2023-08-09 10:02:07,024 - INFO: Seed reads made: get_org_3/seed/animal_mt.initial.fq (305769928 bytes)
2023-08-09 10:02:07,045 - INFO: Making seed reads finished.

2023-08-09 10:02:07,046 - INFO: Checking seed reads and parameters ...
2023-08-09 10:02:07,047 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-08-09 10:02:07,048 - INFO: If the result graph is not a circular organelle genome, 
2023-08-09 10:02:07,049 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2023-08-09 10:03:35,993 - INFO: Pre-assembling mapped reads ...
2023-08-09 10:06:19,921 - INFO: Pre-assembling mapped reads finished.
2023-08-09 10:06:19,922 - INFO: Estimated animal_mt-hitting base-coverage = 6178.61
2023-08-09 10:06:20,368 - INFO: Estimated word size(s): 113
2023-08-09 10:06:20,369 - INFO: Setting '-w 113'
2023-08-09 10:06:20,369 - INFO: Setting '--max-extending-len inf'
2023-08-09 10:06:21,748 - INFO: Checking seed reads and parameters finished.

2023-08-09 10:06:21,768 - INFO: Making read index ...
2023-08-09 10:06:57,670 - INFO: 378377 candidates in all 1122784 reads
2023-08-09 10:06:57,674 - INFO: Pre-grouping reads ...
2023-08-09 10:06:57,675 - INFO: Setting '--pre-w 113'
2023-08-09 10:06:57,739 - INFO: 53097/53097 used/duplicated
2023-08-09 10:07:06,279 - INFO: 1421 groups made.
2023-08-09 10:07:06,341 - INFO: Making read index finished.

2023-08-09 10:07:06,342 - INFO: Extending ...
2023-08-09 10:07:06,343 - INFO: Adding initial words ...
2023-08-09 10:07:50,837 - INFO: AW 5194824
2023-08-09 10:08:02,976 - INFO: Round 1: 378377/378377 AI 159004 AW 5216728
2023-08-09 10:08:09,182 - INFO: Round 2: 378377/378377 AI 159243 AW 5219572
2023-08-09 10:08:16,224 - INFO: Round 3: 378377/378377 AI 159321 AW 5220556
2023-08-09 10:08:22,175 - INFO: Round 4: 378377/378377 AI 159350 AW 5220948
2023-08-09 10:08:27,811 - INFO: Round 5: 378377/378377 AI 159361 AW 5221084
2023-08-09 10:08:35,160 - INFO: Round 6: 378377/378377 AI 159365 AW 5221126
2023-08-09 10:08:42,333 - INFO: Round 7: 378377/378377 AI 159365 AW 5221126
2023-08-09 10:08:42,335 - INFO: No more reads found and terminated ...
2023-08-09 10:09:18,779 - INFO: Extending finished.

2023-08-09 10:09:18,843 - INFO: Separating extended fastq file ... 
2023-08-09 10:09:50,412 - WARNING: No paired reads found?!
2023-08-09 10:09:50,461 - INFO: Setting '-k 21,45,65,85,105'
2023-08-09 10:09:50,462 - INFO: Assembling using SPAdes ...
2023-08-09 10:09:50,487 - INFO: spades.py -t 1  --phred-offset 33 --s1 get_org_3/extended_1_unpaired.fq --s2 get_org_3/extended_2_unpaired.fq -k 21,45,65,85,105 -o get_org_3/extended_spades
2023-08-09 10:22:45,125 - INFO: Assembling finished.

2023-08-09 10:22:47,929 - INFO: Slimming get_org_3/extended_spades/K105/assembly_graph.fastg finished!
2023-08-09 10:22:47,930 - INFO: Slimming assembly graphs finished.

2023-08-09 10:22:47,936 - INFO: Extracting animal_mt from the assemblies ...
2023-08-09 10:22:48,016 - INFO: Disentangling get_org_3/extended_spades/K105/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ... 
2023-08-09 10:22:51,847 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_45377_45383_45185_45171_45165_45159_45153_45143_45235_44218_44212_44627_44681_44639_44651_44659_44667_44677_45097_42394_44498!'
2023-08-09 10:22:51,852 - INFO: Scaffolding disconnected contigs using SPAdes scaffolds ... 
2023-08-09 10:22:51,852 - WARNING: Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph.
2023-08-09 10:22:51,853 - INFO: Disentangling get_org_3/extended_spades/K105/assembly_graph.fastg.extend-animal_mt.fastg as a circular genome ... 
2023-08-09 10:22:53,195 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_45377_45383_45185_45171_45165_45159_45153_45143_45235_44218_44212_44627_44681_44639_44651_44659_44667_44677_45097_42394_44498!'
2023-08-09 10:22:53,202 - INFO: Disentangling get_org_3/extended_spades/K105/assembly_graph.fastg.extend-animal_mt.fastg as a/an animal_mt-insufficient graph ... 
2023-08-09 10:22:54,583 - INFO: Average animal_mt kmer-coverage = 1784.6
2023-08-09 10:22:54,583 - INFO: Average animal_mt base-coverage = 6613.3
2023-08-09 10:22:54,584 - INFO: Writing output ...
2023-08-09 10:22:54,593 - INFO: Writing PATH1 of animal_mt scaffold(s) to get_org_3/animal_mt.K105.scaffolds.graph1.1.path_sequence.fasta
2023-08-09 10:22:54,596 - INFO: Writing GRAPH to get_org_3/animal_mt.K105.contigs.graph1.selected_graph.gfa
2023-08-09 10:22:54,600 - INFO: Result status of animal_mt: 3 scaffold(s)
2023-08-09 10:22:54,654 - INFO: Writing output finished.
2023-08-09 10:22:54,656 - INFO: Please ...
2023-08-09 10:22:54,658 - INFO: load the graph file 'assembly_graph.fastg.extend-animal_mt.fastg' in K105
2023-08-09 10:22:54,658 - INFO: load the CSV file 'assembly_graph.fastg.extend-animal_mt.csv' in K105
2023-08-09 10:22:54,659 - INFO: visualize and confirm the incomplete result in Bandage.
2023-08-09 10:22:54,659 - INFO: If the result is nearly complete, 
2023-08-09 10:22:54,660 - 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
2023-08-09 10:22:54,660 - 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!
2023-08-09 10:22:54,660 - INFO: Extracting animal_mt from the assemblies finished.


Total cost 1446.22 s
Thank you!