Can't produce a correct summary.txt when using annotation module. about mitoz HOT 7 CLOSED

Dear sylviaviii,

I think the reason is that the length of your sequence id is too long. which is not allowed by biopython. the maximum seqid length is 10 or 15 characters, as I remember.

Please shorten your seqid firstly.

Cheers
Guanliang

from mitoz.

Dear sylviaviii,

it is a bug here. and thank you very for reporting this bug.

Could you please replace the file genbank_gene_stat_v2.py in your machine to this
genbank_gene_stat_v2.py.zip

you should decompress it after downloading.

Hope this will help.

Cheers

from mitoz.

Dear Guanliang,

It is helpful with your answer. Thank you!

But these days we have the same situation with different error message. May I ask your favor to tell me how to deal with it? The following is an error report. My sequence are Refseq from NCBI, which are NC_037851.1 and NC_026081.1

2020-01-10 10:05:12
/home/zf/install/miniconda2/envs/mitoz/bin/python3 /home/zf/install/MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py Crassostrea_belcheri_mitoscaf.fa.gbf Crassostrea_belcheri.most_related_species.txt annotate > summary.txt

Traceback (most recent call last):
File "/home/zf/install/MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py", line 238, in
main()
File "/home/zf/install/MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py", line 215, in main
gene_infor, gene_freq = gene_stat(gbfile)
File "/home/zf/install/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:
/home/zf/install/miniconda2/envs/mitoz/bin/python3 /home/zf/install/MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py Crassostrea_belcheri_mitoscaf.fa.gbf Crassostrea_belcheri.most_related_species.txt annotate > summary.txt

from mitoz.

from mitoz.

I'm closing this. You can reopen it if the problem is still there.

from mitoz.

FYI - This bug is still present in the public docker images for versions 2.3 and 2.4_alpha.

from mitoz.

FYI - This bug is still present in the public docker images for versions 2.3 and 2.4_alpha.

I understand your question now. The docker image 2.3 was built years ago and hasn't been updated.

The problem will be solved in next formal version 3.5.

from mitoz.