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error when using "generate_conf.py" to prepare input files of WGDI

Open sanvva opened this issue 2 years ago • 0 comments

Genome sequences and annotation gff files of Apostasia shenzhenica and Phalaenopsis equestris were downloaded from: https://www.ncbi.nlm.nih.gov/genome/66931 ftp://ftp.genomics.org.cn/pub/Orchid_Phalaenopsis_equestris/

python generate_conf.py -p Ash Ashenzhenica.genome.fasta Ashenzhenica.gene.gff
python generate_conf.py -p Peq Pequestris.genome.fasta Pequestris.gene.gff

Errors: 1. Traceback (most recent call last): File "generate_conf.py", line 117, in chrom=chrom,lens=lens,count=gene_count[chrom]), file=len_file) KeyError: 'KZ451892.1'

Traceback (most recent call last): File "generate_conf.py", line 89, in gene_dict, tx_pos_dict, CDS_dict= parse_gff( args.gff ) File "generate_conf.py", line 67, in parse_gff tx_parent = re.search(r'Parent=(.*?)[;\n]',content[8]).group(1) AttributeError: 'NoneType' object has no attribute 'group'

sanvva avatar Mar 03 '22 01:03 sanvva