linzhi2013
commented
5 years ago Hi Marsel,
What species do you have? The genetic code of mitochondrial genome for Chordata should be 2, not 1.
Did you already obtain the mitogenome sequence? If yes, you may just annotate the sequence and see if it was the problem with the --genetic_code 1? annotate is quite fast.
Cheers, Guanliang
Hi Guanliang!
I installed MitoZ by docker (v2.3 and 2.4a) and tried to analyze mitogenome but I see always the same error.
Variants of command line: 1) python3 /app/release_MitoZ_v2.4-alpha/MitoZ.py all --genetic_code 1 --clade Chordata --thread_number 13 --outprefix duck-01 --fastq1 duck-01_S10_L001_R1_001.fastq.gz --fastq2 duck-01_S10_L001_R2_001.fastq.gz --fastq_read_length 300 --insert_size 300 --run_mode 2 --filter_taxa_method 1 --requiring_taxa 'Chordata'
2) python3 /app/release_MitoZ_v2.4-alpha/MitoZ.py annotate --fastafile duck.fa --genetic_code 1 --clade Chordata --thread_number 13 --outprefix duck.fa
3) python3 /app/release_MitoZ_v2.3/MitoZ.py annotate --fastafile duck.fa --genetic_code 1 --clade Chordata --thread_number 13 --outprefix duck.fa
In all cases it was error such type: /app/anaconda/bin/python3 /app/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py duck-01_mitoscaf.fa.gbf duck-01.most_related_species.txt all > summary.txt
Traceback (most recent call last): File "/app/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py", line 238, in
main()
File "/app/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py", line 215, in main
gene_infor, gene_freq = gene_stat(gbfile)
File "/app/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py", line 97, in gene_stat
print(ass_num, "Warning: NO gene or product tag! this gene is not output!\n")
NameError: name 'ass_num' is not defined
Error occured when running command:
/app/anaconda/bin/python3 /app/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py duck-01_mitoscaf.fa.gbf duck-01.most_related_species.txt all > summary.txt
Could you help with this bug?
Best wishes, Marsel