align.seqs: number of read in sequences

Hello, I am running align.seqs and have about 800K sequences to be aligned. I noticed that Mothur printed out the number of sequences read in to be about 157,000. Did something go wrong with reading in my sequences?

THe program is running fine with no issue but now I am concerned that it is not aligning all sequences.

Thank you.

Did you use 5 processors? The number that is outputted is the number of sequences that were aligned on each processor. You could always run screen.seqs on the output of align.seqs and make sure that you have the same number of sequences as when you run screen.seqs on the input file.


I have the same problem, I have around 2500000 seqs but after align with gthe silva.seed_v132.align and made summary.seqs the number of sequences is 5000000. I have 98 libraries and i am using 30 processors. What can I do? i am stuck for 15 days

I’d be happy to help you track down the issue. Could you send your log file to