cut-range --skip=1250 < C1.P1.fastas | alignment-max > P1-max.fasta
And this command did not work (No such file or directory/ No alignment found).
So, I tried:
cut-range --skip=1250 < Analysis_ITS1_BAliPhy-1/C1.P1.fastas | alignment-max > P1-max.fasta
And then I got this message:
alignment-max: Error! Sequence 26: length 133 differs from expected length 129
I have tried with the C1.P1.fastas file of each folder (-1, -2, etc.), getting always the same error with different values. Interestingly, the error always appeared on sequences 15-26, which I guess correspond to the ancestral sequences (AXX).
I have also tried with the six alignments at once:
cut-range --skip=1250 < Analysis_ITS1_BAliPhy-1/C1.P1.fastas Analysis_ITS1_BAliPhy-2/C1.P1.fastas Analysis_ITS1_BAliPhy-3/C1.P1.fastas Analysis_ITS1_BAliPhy-4/C1.P1.fastas Analysis_ITS1_BAliPhy-5/C1.P1.fastas Analysis_ITS1_BAliPhy-6/C1.P1.fastas | alignment-max > P1-max.fasta
And I got the same error again (I have not found in the tutorial or other documentation how to compute the alignment from various .fastas files, this is why I tried with the previous command, but maybe it is wrong).
I have changed the value of the burn-in, with no success (same error).
The weird thing is that I have checked the .fastas files, and I do not see any difference in sequence length, neither in the original sequences nor in the ancestral sequences. I repeated the same analysis twice, in case I was getting any random error or any file was miswritten. I have also checked the sequence names, and they do not contain any space, special characters or dashes; only letters, numbers and underscores.
I am using version 3.3. in Cygwin (Windows 10).
Any idea of what I am doing wrong?
Thank you very much!