Not aligning all sequences?

Hi -

I am pretty sure this is not a bug in the software but a problem with my computing potential. That said I wanted to be certain…

-I have a fasta file of 210928 - a mixture of pyrotag and full length sanger reads (after unique.seqs and screen.seqs)
-I run the following:

align.seqs(candidate=flpyro.unique.good.fas, template=core_set_aligned.imputed.fasta, flip=t, processors=4)

-And get the following:

Reading in the core_set_aligned.imputed.fasta template sequences… DONE.
Aligning sequences…
Some of you sequences generated alignments that eliminated too many bases, a list is provided in flpyro.unique.good.flip.accnos. If the reverse compliment proved to be better it was reported.
It took 2265 secs to align 210928 sequences.

Problem is that only the first 166275 sequences align even though the Terminal message reports all sequences align. The last 44652 are left out. I do not have any more RAM so I am unable to confirm that lack of RAM is the problem.

So, I performed 2 separate alignments. Is it ok to concatenate the alignment files? Is there another solution?


It’s probably not a RAM issue. I suspect it’s a bug we found that occurs if the sequence you are about to align contains more bases than the longest sequence in your template. With multiple processors you don’t see the bad_access error because the process just dies. We have corrected the issue in 1.8 releasing early February. You can send me an email at if you want the fix early.

btw, I have tested the fix and it does indeed seem to work.

Indeed - it works fine for me as well