ambiguous messages from aligner regarding flip.accnos

mothur bugs
1

Just wanted to note some ambiguous messages from the aligner when using “flip=t”.

Some of you sequences generated alignments that eliminated too many bases, a list is provided in sequences.flip.accnos. If the reverse compliment proved to be better it was reported.

# cat sequences.flip.accnos
CP002042
AJ867032
AJ867034        reverse complement did NOT produce a better alignment, please check sequence.
AM261868

The above implies that the reverse-complemented sequences for CP002042, AJ867032, and AM261868 produced a better alignment than their original sequences, and were included that way in the resulting alignment. If this is correct, could you state that explicitly in these messages? From an end user perspective, it is not clear how these were ultimately treated (except for AJ867034, which is explicitly stated).

2

Thanks for the suggestion. In version 1.13.0, the output file will look like:

CP002042 reverse complement produced a better alignment, so mothur used the reverse complement.
AJ867032 reverse complement produced a better alignment, so mothur used the reverse complement.
AJ867034 reverse complement did NOT produce a better alignment so it was not used, please check sequence.
AM261868 reverse complement produced a better alignment, so mothur used the reverse complement.

3

Thank you, these look good.