关于mp_import_metaphlan中输入treefile错误的问题
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
Research direction
Start by reproducing the mp_import_metaphlan call with merged_abundance_table.txt and mpa_vOct22_CHOCOPhlAnSGB_202212.nwk under MicrobiotaProcess v1.12.3. Inspect the reported parent validation errors and compare the resulting texatree and otutree objects; the issue is resolved when the supported input behavior and generated tree objects are clear.
Written by the indexing model from the issue text.
Description
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
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