The first character of the accession numbers in my FASTA files are being dropped in all of my output files.
align.seqs(candidate=test.fasta, template=reference.fasta, align=needleman)
reference.fasta is the Greengenes reference alignment.
test.fasta and the results are attached.
As a workaround, I am now prepending an additional character to each accession number.
I am using mothur v1.11.0, compiled with OpenMPI 1.4.2 support on 32-bit Linux.
Update 2010-07-30: I am still experiencing this problem on v1.12.1. I’m now on 64-bit Linux and have recompiled with and without MPI support.
This problem occurs only when compiled with MPI support.
The dist.seqs command isn’t affected by this problem.
Update 2010-08-11: This is still a problem with v1.12.3. Others are also reporting this issue. See post truncated seq IDs after filter?