KeyError: 'animal_mt'

[sihellem]

Hi, @Kinggerm,

I am trying to assemble the mitochondrion from my termite using the following code:

get_organelle_from_reads.py -1 CIVT039_S65_R1_001_val_1.fq.gz -2 CIVT039_S65_R2_001_val_2.fq.gz -o CIVT039 -s Astalotermes_genome.fasta.txt --genes Astalotermes_gene_features_sequence.txt -R 3 -k 21,45,65,85,105 -F animal_mt

Using this configuration:

GetOrganelle v1.6.2

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 3.7.1 (default, Dec 14 2018, 19:28:38) [GCC 7.3.0]
Python libs: numpy 1.16.4; sympy 1.4; scipy 1.3.0
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30

However, after the assembly step using SPAdes and the slimming of assembly graphs, I get the following:

2019-07-02 14:51:57,241 - INFO: Extracting animal_mt from the assemblies ...
2019-07-02 14:51:57,243 - INFO: Disentangling CIVT039_S65_R1_001_val_1_output/filtered_spades/K105/assembly_graph.fastg.extend-Astalotermes_gene_features_sequence.txt.fastg as a circular genome ...
2019-07-02 14:51:57,249 - ERROR:
Traceback (most recent call last):
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3340, in extract_organelle_genome
temp_graph=graph_temp_file)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3302, in disentangle_assembly
acyclic_allowed_in=here_acyclic_allowed, verbose_in=here_verbose, in_temp_graph=temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/pipe_control_func.py", line 85, in func_modified
r = func(*args, **kwargs)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3189, in disentangle_inside
temp_graph=in_temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1769, in find_target_graph
self.parse_tab_file(tab_file, mode=mode, type_factor=type_factor, log_handler=log_handler)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1250, in parse_tab_file
if len(self.tagged_vertices[mode]) == 0:
KeyError: 'animal_mt'
2019-07-02 14:51:57,254 - ERROR:
Traceback (most recent call last):
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3340, in extract_organelle_genome
temp_graph=graph_temp_file)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3302, in disentangle_assembly
acyclic_allowed_in=here_acyclic_allowed, verbose_in=here_verbose, in_temp_graph=temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/pipe_control_func.py", line 85, in func_modified
r = func(*args, **kwargs)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3189, in disentangle_inside
temp_graph=in_temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1769, in find_target_graph
self.parse_tab_file(tab_file, mode=mode, type_factor=type_factor, log_handler=log_handler)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1250, in parse_tab_file
if len(self.tagged_vertices[mode]) == 0:
KeyError: 'animal_mt'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3803, in main
options=options)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3353, in extract_organelle_genome
sys.exit()
SystemExit

Total cost 317.57 s
Please email jinjianjun@mail.kib.ac.cn or phylojin@163.com if you find bugs!
Please provide me with the get_org.log.txt file!

Do you have any idea of what's happening here?

Thanks a lot in advance!

[Kinggerm]

Thanks for pointing out this bug. I will fix this very soon.
Currently, you could rename Astalotermes_gene_features_sequence.txt to animal_mt.fasta and make it work (if you use --continue option to resume, you should firstly remove *csv files previously produced). I would let you know once I fixed this, after which there is no need to do this pre-renaming.
Sorry for the inconvenience and thanks again for letting me know!

Best,
Jianjun

[sihellem]

Hello Jianjun,

Thanks, it did work indeed!

Cheers,
Simon

[Kinggerm]

Fix it in 1.6.2a. No need to rename anymore.
But I am in the field these days and only get a small dataset to test. Let me know if it doesn't work for you.

Cheers,
Jianjun

[duanyuj]

Dear Jianjun,

I have a little question, what exactly does -- genes mean, while you enter a command.

I can't find an explanation in the help.

Looking forward to your help.

Thanks.

[Kinggerm]

Dear Jianjun,

I have a little question, what exactly does -- genes mean, while you enter a command.

I can't find an explanation in the help.

Looking forward to your help.

Thanks.

You can type get_organelle_from_reads.py --help rather than get_organelle_from_reads.py -h to get a verbose version of all options, where you can find illustration of --genes as follows:

--genes=GENES_FASTA
                   Followed with a customized database (a fasta file or
                   the base name of a blast database) containing or made
                   of ONE set of protein coding genes and ribosomal RNAs
                   extracted from ONE reference genome that you want to
                   assemble. Should be a list of databases split by
                   comma(s) on a multi-organelle mode, with the same list
                   length to organelle_type (followed by '-F'). This is
                   optional for any organelle mentioned in '-F' but
                   required for 'anonym'. By default, certain database(s)
                   in /Users/Kinggerm/.pyenv/versions/anaconda3-5.3.1/lib
                   /python3.7/site-packages/GetOrganelleLib/LabelDatabase
                   would be used contingent on the organelle types chosen
                   (-F). The default value no longer holds when '--genes'
                   or '--ex-genes' is used.