sequence contains only gap

Question

[saifulislam99121]

Hi, I was trying CFSAN pipeline for listeria. When building the tree, I got this error-

" WARNING: 25 sequences contain more than 50% gaps/ambiguity
****  TOTAL                         77.30%  0 sequences failed composition chi2 test (p-value<5%; df=3)
WARNING: Sequence austria_2012_human contains only gaps or missing data
WARNING: Sequence bangladesh_2022_human contains only gaps or missing data
WARNING: Sequence mexico_2018_food contains only gaps or missing data
WARNING: Sequence spain_2019_animal contains only gaps or missing data
ERROR: Some sequences (see above) are problematic, please check your alignment again"

Any suggestions?

[manaswwm]

I have never used this tool but is the error message not obvious? The said sequences contain only missing data which means you will not be able to build a phylogenetic tree with those sequences, look at the alignments again and either remove those sequences or choose a different genomic region (?) where the alignment is better.