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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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error #35

Closed 123123456abc closed 1 year ago

123123456abc commented 2 years ago

Dear author, I encountered an error when running the software.Encountered a problems，could you please help me check the reason? I have attached the command line and log below, thank you very much

Traceback (most recent call last): File "/home/appl/anaconda3/envs/TEsorter/bin/TEsorter", line 10, in sys.exit(main()) File "/home/appl/anaconda3/envs/TEsorter/lib/python3.10/site-packages/TEsorter/app.py", line 1014, in main pipeline(Args()) File "/home/appl/anaconda3/envs/TEsorter/lib/python3.10/site-packages/TEsorter/app.py", line 174, in pipeline for rc in Classifier(gff, db=args.hmm_database, fout=fc): File "/home/appl/anaconda3/envs/TEsorter/lib/python3.10/site-packages/TEsorter/app.py", line 414, in classify order, superfamily, max_clade, coding = self.identify_rexdb(genes, names) File "/home/appl/anaconda3/envs/TEsorter/lib/python3.10/site-packages/TEsorter/app.py", line 430, in identify_rexdb order, superfamily = self._parse_rexdb(max_clade) File "/home/appl/anaconda3/envs/TEsorter/lib/python3.10/site-packages/TEsorter/app.py", line 470, in _parse_rexdb logger.warning( 'unknown clade: {}'.format(max_clade) ) NameError: name 'max_clade' is not defined

zhangrengang commented 2 years ago

Hi @123123456abc, can you send me your input fasta file via email (zhangrengang@ori-gene.cn)? This error should not be reach.

123123456abc commented 2 years ago

I sent you a data,the email(1509981823@qq.com),thanks.

zhangrengang commented 2 years ago

@123123456abc It is because there are special characters (; and =) that confused the gff3 attribute fields:

Scaffold_387868;HRSCAF=412686   TEsorter        CDS     281162955       281163185       52.6    -       1      ID=Scaffold_387868;HRSCAF=412686:281162954-281163490|Class_I/LTR/Ty1_copia/Tork:Ty1-RH;gene=RH;clade=Tork;evalue=4.7e-16;coverage=58.7;probability=0.92
Scaffold_387868;HRSCAF=412686   TEsorter        CDS     281165562       281165999       119.9   -       2      ID=Scaffold_387868;HRSCAF=412686:281165296-281166233|Class_I/LTR/Ty1_copia/Tork:Ty1-RT;gene=RT;clade=Tork;evalue=1.2e-36;coverage=49.6;probability=0.87

The simplest way for you to fix it is replacing these characters:

sed 's/;/_/;s/=/_/' test.fa > test.fa.rename