Can't produce a correct summary.txt when using annotation module.

[sylviaviii]

I was annotating for about 50 species with MitoZ. But there are about 10 species can't produce a correct summary.txt. The following is an error report. I think the main reason is "Name and length collide in the LOCUS line". Why this situation happened?

2019-10-01 10:29:06
/home/zf/install/miniconda3/envs/mitozEnv/bin/python3 /home/zf/install/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py 1_Poeciloneta_variegata_mitoscaf.fa.gbf 1_Poeciloneta_variegata.most_related_species.txt annotate > summary.txt

Traceback (most recent call last):
File "/home/zf/install/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 238, in
main()
File "/home/zf/install/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 202, in main
seqid_len_topology_relatedSP = get_seq_topology_and_related_sp(gbfile=gbfile, closely_related_sp_file=closely_related_sp_file)
File "/home/zf/install/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 173, in get_seq_topology_and_related_sp
for rec in SeqIO.parse(gbfile, 'gb'):
File "/home/zf/install/miniconda3/envs/mitozEnv/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 609, in parse
for r in i:
File "/home/zf/install/miniconda3/envs/mitozEnv/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 480, in parse_records
record = self.parse(handle, do_features)
File "/home/zf/install/miniconda3/envs/mitozEnv/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 464, in parse
if self.feed(handle, consumer, do_features):
File "/home/zf/install/miniconda3/envs/mitozEnv/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 431, in feed
self._feed_first_line(consumer, self.line)
File "/home/zf/install/miniconda3/envs/mitozEnv/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 1285, in _feed_first_line
'Name and length collide in the LOCUS line:\n' + line
AssertionError: Name and length collide in the LOCUS line:
LOCUS 1_Poeciloneta_variegata14332 bp DNA linear 01-OCT-2019

Error occured when running command:
/home/zf/install/miniconda3/envs/mitozEnv/bin/python3 /home/zf/install/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py 1_Poeciloneta_variegata_mitoscaf.fa.gbf 1_Poeciloneta_variegata.most_related_species.txt annotate > summary.txt

[linzhi2013]

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

[sylviaviii]

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

[linzhi2013]

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

[sylviaviii]

It works! Thank you 

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人:&nbsp;"Guanliang MENG"<notifications@github.com&gt;; 发送时间:&nbsp;2020年1月10日(星期五) 中午1:50 收件人:&nbsp;"linzhi2013/MitoZ"<MitoZ@noreply.github.com&gt;; 抄送:&nbsp;"DJ"<71272550@qq.com&gt;;"Author"<author@noreply.github.com&gt;; 主题:&nbsp;Re: [linzhi2013/MitoZ] Can't produce a correct summary.txt when using annotation module. (#24) 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[linzhi2013]

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

[dleopold]

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

[linzhi2013]

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.