eggNOG 保留蛋白序列时提示同一 ID 被多个一级特征使用,而子特征的 Parent 属性没有得到相应更新,导致注释关系不明确的问题,该怎么解决

老师我在进行如下步骤时,会有warning提示,gff和fasta都是非模式物种ncbi数据库染色体水平的组装,ga_protein_coding.gff3文件正常生成了,请问warning对结果有影响吗,应该如何解决?谢谢!

agat_sp_filter_feature_by_attribute_value.pl --gff $gff --attribute gene_biotype --value protein_coding -t '!' -o ga_protein_coding.gff3


Indeed we changed the ID for this L1 feature to be unique but we do not change the Parent attribute of the child features to reflect this change. Why? because we do not know to which L1 the child feature was part-of because several Parent have similar ID. @ the feature is: NC_057868.1 RefSeq cDNA_match 2670480 2670611 . + . ID "nbis-cdna_match-8" ; Target "XM_044118420.1 1144 1275 +" ; for_remapping 2 ; gap_count 1 ; num_ident 5340 ; num_mismatch 0 ; pct_coverage "99.9626" ; pct_coverage_hiqual "99.9626" ; pct_identity_gap "99.9626" ; pct_identity_ungap 100 ; rank 1 original id: 6c7537ad-e0c2-47d5-8dc4-6ff9f4d4de36 WARNING level1: This feature level1 is not a duplicate but has an ID already used. /!\ AGAT might mix up the child features and create chimeric records. Indeed we changed the ID for this L1 feature to be unique but we do not change the Parent attribute of the child features to reflect this change. Why? because we do not know to which L1 the child feature was part-of because several Parent have similar ID. @ the feature is: NC_057868.1 RefSeq cDNA_match 2671425 2671546 . + . ID "nbis-cdna_match-9" ; Target "XM_044118420.1 1276 1397 +" ; for_remapping 2 ; gap_count 1 ; num_ident 5340 ; num_mismatch 0 ; pct_coverage "99.9626" ; pct_coverage_hiqual "99.9626" ; pct_identity_gap "99.9626" ; pct_identity_ungap 100 ; rank 1 original id: 6c7537ad-e0c2-47d5-8dc4-6ff9f4d4de36 WARNING level1: This feature level1 is not a duplicate but has an ID already used. /!\ AGAT might mix up the child features and create chimeric records. Indeed we changed the ID for this L1 feature to be unique but we do not change the Parent attribute of the child features to reflect this change. Why? because we do not know to which L1 the child feature was part-of because several Parent have similar ID. @ the feature is: NC_057868.1 RefSeq cDNA_match 2673147 2673251 . + . ID "nbis-cdna_match-10" ; Target "XM_044118420.1 1398 1502 +" ; for_remapping 2 ; gap_count 1 ; num_ident 5340 ; num_mismatch 0 ; pct_coverage "99.9626" ; pct_coverage_hiqual "99.9626" ; pct_identity_gap "99.9626" ; pct_identity_ungap 100 ; rank 1 original id: 6c7537ad-e0c2-47d5-8dc4-6ff9f4d4de36 WARNING level1: This feature level1 is not a duplicate but has an ID already used. /!\ AGAT might mix up the child features and create chimeric records. Indeed we changed the ID for this L1 feature to be unique but we do not change the Parent attribute of the child features to reflect this change. Why? because we do not know to which L1 the child feature was part-of because several Parent have similar ID.


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