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关于mp_import_metaphlan中输入treefile错误的问题 #95

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Brynnhildr opened this issue Jul 17, 2023 · 2 comments
Open

关于mp_import_metaphlan中输入treefile错误的问题 #95

Brynnhildr opened this issue Jul 17, 2023 · 2 comments

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@Brynnhildr
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各位老师好!我在使用 mp_import_metaphlan 输入metaphlan4的相对丰度的输出结果文件时,指定了我metaphlan4对应的数据库的进化树文件 mpa_vOct22_CHOCOPhlAnSGB_202212.nwk 。但是输入报错,具体如下:

metaphlan_data <- mp_import_metaphlan("merged_abundance_table.txt",linenum=2,treefile = "mpa_vOct22_CHOCOPhlAnSGB_202212.nwk")
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
Warning messages:
1: The number of features in otu table is not equal the number of tips in otu tree.
• The same features will be extract automatically !
2: In drop.tip.phylo(phy = list(edge = c(30212L, 30213L, 30213L, 30214L, :
drop all tips of the tree: returning NULL
3: In drop.tip.phylo(collapse.singles = FALSE, phy = list(edge = c(787, :
drop all tips of the tree: returning NULL

最终得到的MPSE,除了些样本名的信息之外,texatree、otutree都没能成功生成。 我在bioconductor上安装版本是MicrobiotaProcess v1.12.3。请问老师,这是否是因为目前的版本还不能支持metaphlan4的进化树,只能支持到mpa_v30_CHOCOPhlAn_201901_species_tree.nwk metaphlan3的进化树?或者还是因为一些其它的问题?

感谢您的回复与帮助! @xiangpin

@xiangpin
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metaphlan4的进化树目前还没支持,后续我再更新一下。

@Brynnhildr
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好的,感谢回复,期待后续更新!

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