老师你好,
我删除了显示Families with largest size differentials的家族,重新进行分析后。又报出了新的差异过大的家族,连续删除运行了几次依然报错。 请问是怎么回事?
Families with largest size differentials:
OG0000000: 848
OG0000089: 166
OG0000007: 134
OG0000055: 122
OG0000033: 106
OG0000006: 104
OG0000051: 103
OG0000053: 99
OG0000309: 94
OG0000003: 91
OG0000016: 88
OG0000025: 82
OG0000326: 82
OG0000071: 79
OG0000429: 75
OG0000569: 74
OG0000005: 73
OG0000285: 73
OG0000023: 72
OG0000097: 66
作者回复:if families are changing too rapidly, it becomes hard to infer their most likely ancestral state, and therefore whether there have been gains or losses on a specific branch. But if you’d like to get a non-exact idea of what’s going on, you could try analyzing these families while setting lambda to a very low value (for instance, 0.0001)—do not search for lambda. This will tell you what the ancestral sizes were under a model where the families are evolving slowly, but should be an approximation of their true size.
#可以过滤掉这些基因家族, 再做分析
python3 /share/work/biosoft/CAFE/CAFE5/tutorial/clade_and_size_filter.py -i input.tab -o input.tab.filtered -s
###如果报错:Families with largest size differentials: https://www.omicsclass.com/question/5581
cat cafe5.log |grep "^OG" |awk -F":" '{print $1}' >family.remove.id.txt
grep -v -f family.remove.id.txt input.tab >input.tab.new
#再次运行
cafe5 --infile input.tab.new --tree input.tree --output_prefix cafe_result --cores 20 -k 3 -p --pvalue 0.05 &>cafe5.log1
如果觉得我的回答对您有用,请随意打赏。你的支持将鼓励我继续创作!