Error message from aligner

When I attempt to align my trimmed 16S sequences (V5-V6, ~330bp), I keep getting the following message:

Error: Could not open ~/BTHlast/BTH.trim.unique.align
Error: Could not open ~/BTHlast/
Error: Could not open ~/BTHlast/BTH.trim.unique.flip.accnos436.temp
Error: Could not open ~/BTHlast/BTH.trim.unique.flip.accnos437.temp
Error: Could not open ~/BTHlast/BTH.trim.unique.flip.accnos
Some of you sequences generated alignments that eliminated too many bases, a list is provided in ~/BTHlast/BTH.trim.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well.
It took 33 secs to align 3811 sequences.

An ‘align’ file is not generated, nor is an ‘accnos’ file. accnos436 and accnos437, however, are generated in the correct directory. I don’t know why they cannot be opened. I’ve also tried changing the flip parameter to T, but to no avail.

Start End NBases Ambigs Polymer
Minimum: 1 314 314 0 4
2.5%-tile: 1 325 325 0 4
25%-tile: 1 329 329 0 4
Median: 1 331 331 0 5
75%-tile: 1 332 332 0 5
97.5%-tile: 1 334 334 0 6
Maximum: 1 372 372 0 8

of Seqs: 3811

I just noticed that in the report.temp file my query lengths are indicated to range from 2 to 100 (they are all actually ~330).

Could you send the logfile and your input files to

Just sent it. Thanks

Mothur was not able to open your files because it could not resolve the ~ in the filename. The fix will be part of 1.13.0. Thanks for bringing it to our attention.