Hi, I can not run guidemarker using genome fasta +gff file. Appreciate any help.

[hz-mswang]

2022-11-10 15:34:20,592 root ERROR GuideMaker terminated with errors. See the log file for details.
Traceback (most recent call last):
File "/home/shuang/miniconda3/envs/gmenv/lib/python3.9/site-packages/guidemaker/cli.py", line 193, in main
anno.get_annotation_features()
File "/home/shuang/miniconda3/envs/gmenv/lib/python3.9/site-packages/guidemaker/core.py", line 761, in get_annotation_features
if not feat_key in feature_dict:
UnboundLocalError: local variable 'feat_key' referenced before assignment

gff example:
JAIZPG010000102.1 AUGUSTUS gene 60 1208 0.39 - . ID=gene-alt2500001;Name=alt2500001;gbkey=Gene;gene_biotype=protein_coding;locus_tag=alt2500001
JAIZPG010000102.1 AUGUSTUS mRNA 60 1208 0.39 - . ID=rna-gnl|WGS:LPVP|mrna.alt2500001;Parent=gene-alt2500001;gbkey=mRNA;locus_tag=alt2500001;orig_protein_id=gnl|WGS:LPVP|alt2500001;orig_transcript_id=gnl|WGS:LPVP|mrna.alt2500001;product=alt2500001
JAIZPG010000102.1 AUGUSTUS CDS 60 234 0.96 - 1 ID=cds-alt2500001;Parent=rna-gnl|WGS:LPVP|mrna.alt2500001;Dbxref=NCBI_GP:alt2500001;Name=alt2500001;gbkey=CDS;locus_tag=alt2500001;orig_transcript_id=gnl|WGS:LPVP|mrna.alt2500001;product=alt2500001;protein_id=alt2500001

[arivers]

Could you give me the command you ran to produce this error? If you are able to post a link to the data files that would be helpful too. I think it has to do with the set of tags your annotation produced in the gff. Guidemaker guesses from a list of standard tags but if they are non-standard you have to provide them on the command line.

[hz-mswang]

Thank you for your reply. The command I used is:"guidemaker -f hznu325-genome.masked.fasta -g hznu325.gff3 -o aa325 --threads 28 -p NGG". You can find the data here----"https://doi.org/10.6084/m9.figshare.17036435". The guidemarker can run the command with gff file or gbk file downloaded from NCBI, however, it reports errors when I used my own data. I have tried to put those tags in the gff file (see the example in my first comment), but so far, no success.

…

-----原始邮件----- 发件人:"Adam Rivers" ***@***.***> 发送时间:2022-11-10 23:48:03 (星期四) 收件人: USDA-ARS-GBRU/GuideMaker ***@***.***> 抄送: hz-mswang ***@***.***>, Author ***@***.***> 主题: Re: [USDA-ARS-GBRU/GuideMaker] Hi, I can not run guidemarker using genome fasta +gff file. Appreciate any help. (Issue #18) Could you give me the command you ran to produce this error? If you are able to post a link to the data files that would be helpful too. I think it has to do with the set of tags your annotation produced in the gff. Guidemaker guesses from a list of standard tags but if they are non-standard you have to provide them on the command line. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

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[arivers]

I'll take a look at it when I'm back at work next week.

[arivers]

I downloaded your data and ran it successfully on my computer. The only thing I changed was adding the line ##gff-version=3 to your gff file generated by AGUSTUS. I also noticed that the example gff has contig id's that look like this JAIZPG010000102.1 and the files you sent have contig ids that look like this NODE_20_length_608411_cov_17.089849. Having mismatches in the contig names may have caused the issue.