Is it dropping all of the loci because they all have fewer than 3 tips? It's not clear to me from the above how many lines are in the log file and/or how many loci you are attempting to input to phyluce_align_seqcap_align. Trimming could also be causing an issue - you could try to pass the --no-trim flag and see what happens, as well.
Is it dropping all of the loci because they all have fewer than 3 tips? It's not clear to me from the above how many lines are in the log file and/or how many loci you are attempting to input to
phyluce_align_seqcap_align. Trimming could also be causing an issue - you could try to pass the--no-trimflag and see what happens, as well.