Entering edit mode
Hi,
I have run DADA2 algorithm for my original data and in order to build phylogenetic tree I am trying to perform alignment for v3-4 region of my 19153 unique sequences using this code:
library(DECIPHER)
#Run Sequence Alignment (MSA) using DECIPHER
alignment <- AlignSeqs(DNAStringSet(sequences), anchor=NA)
But it stuck at this alignment step (12 hours have passed):
Aligning Sequences:
================================================================================
Time difference of 193.47 secs
Iteration 1 of 2:
Determining distance matrix based on alignment:
================================================================================
Time difference of 189.15 secs
Reclustering into groups by similarity:
================================================================================
Time difference of 45.95 secs
Realigning Sequences:
================================================================================
Time difference of 149 secs
Iteration 2 of 2:
Determining distance matrix based on alignment:
================================================================================
Time difference of 185.69 secs
Reclustering into groups by similarity:
================================================================================
Time difference of 47.76 secs
Realigning Sequences:
================================================================================
Time difference of 11.27 secs
Refining the alignment:
================================================================================
Time difference of 0.66 secs
I am wondering whether someone can help me to fix this, or if have any other suggestions.
Thanks in advance.
It is unclear where you are stuck in the output above. It looks like the process finished, because refinement is the last step.
Yes, but it was on this even after 24 hours. After alignment, it was supposed to save the output as an R object. I thought maybe 19153 is a giant number of sequences for this function.
Try this:
Because that will skip the only step that occurs after the progress bar finishes, as in your output above.