Sequence Length

[Justin Lewandowski]

Hey Dr. Hey and everyone,

I just started using ima2, and when I try to run it I get an error
message that in locus 0 (sreb) the sequence length is shorter than
expected. However, I have the length listed as 951 bp and double
checked that that’s definitely how long the sequence is. I’m not sure
if it has anything to do with the fact that there are two alleles, but
I used a separate line for each. I also made sure to have 10 spaces
in the sample name. Any ideas what could be causing this? Thanks a
bunch!

Here’s how I have it entered:

sreb 3 3 4 951 I 1.0
pop0_1
CAACTGACCTCTTTGGGTTTCATCATCGGAGTCGGTGTGGTTGGAAACCTCCTGATCTCCATCCTGCTGGTCAAAGACAAGAGCCTGCACCGGGCGCCCTACTATTTCCTGCTGGACCTGTGCGCCTCTGACATCCTGCGCTCCGCCATCTGCTTCCCATTTGTCTTCACGTCGGTCAAGAATGGATCAGCCTGGACCTATGGCACGTTGACCTGCAAAGTGATCGCCTTTCTGGGTGTGCTCTCCTGTTTCCACACGGCGTTTATGCTATTCTGTGTCAGCGTCACGCGCTACCTAGCCATCGCACACCACCGTTTCTACACCAAGAGGCTGACCTTCTGGACCTGTCTAGCCGTCATCTGCATGGTGTGGACGTTGTCAGTGGCGATGGCGTTCCCGCCCGTGCTAGACGTAGGGACGTACTCTTTCATCCGGGAGGAGGACCAGTGCACGTTCCAGCACCGTTCGTTCAGGGCGAACGACTCGCTGGGCTTCATGCTCCTGCTGGCGCTCATCCTCCTGGCCACACAGCTGGTTTACCTCAAGCTCATCTTCTTCGTCCACGACCGTCGAAAGATGAAGCCTGTCCAGTTCGTGCCTGCTGTCAGCCAGAACTGGACCTTCCACGGGCCAGGCGCCAGCGGCCAGGCGGCGGCAAACTGGCTGGCCGGATTCGGGCGAGGCCCCACCCCGCCTACCCTGCTGGGCATCCGGCAGAACAGCAACGCAGCGGGCCGCAGGCGTCTACTGGTGTTGGATGAGTTCAAAACAGAGAAGAGGATTAGTAGGATGTTCTACATCATGACGTTTTTCTTCCTGGCGCTGTGGGGGCCCTATCTGGTCGCCTGCTACTGGCGGGTGTTTGCCAGGGGCCCCGTGGTCCCTGGGGGCTACCTGACGGCAGCCGTGTGGATGAGCTTTGCCCAGGCTGGGGTCAATCCTTTCATCTGC
CAACTGACCTCTTTGGGTTTCATCATCGGAGTCGGTGTGGTTGGAAACCTCCTGATCTCCATCCTGCTGGTCAAAGACAAGAGCCTGCACCGGGCGCCCTACTATTTCCTGTTGGACCTGTGCGCCTCTGACATCCTGCGCTCCGCCATCTGCTTCCCCTTTGTCTTCACGTCGGTCAAGAATGGATCAGCCTGGACCTATGGCACGTTGACCTGCAAAGTGATCGCCTTTCTGGGTGTGCTCTCCTGTTTCCACACGGCGTTTATGCTATTCTGTGTCAGCGTCACGCGCTACCTAGCCATCGCACACCACCGTTTCTACACCAAGAGGCTGACCTTCTGGACCTGTCTAGCCGTCATCTGCATGGTGTGGACGTTGTCAGTGGCGATGGCGTTCCCGCCCGTGCTAGACGTAGGGACGTACTCTTTCATCCGGGAGGAGGACCAGTGCACGTTCCAGCACCGTTCGTTCAGGGCGAACGACTCGCTGGGCTTCATGCTCCTGCTGGCGCTCATCCTCCTGGCCACACAGCTGGTTTACCTCAAGCTCATCTTCTTCGTCCACGACCGTCGAAAGATGAAGCCTGTCCAGTTCGTGCCTGCTGTCAGCCAGAACTGGACCTTCCACGGGCCAGGCGCCAGCGGCCAGGCGGCGGCAAACTGGCTGGCCGGATTCGGGCGAGGCCCCACCCCGCCTACCCTGCTGGGCATCCGGCAGAACAGCAACGCAGCGGGCCGCAGGCGTCTACTGGTGTTGGATGAGTTCAAAACAGAGAAGAGGATTAGTAGGATGTTCTACATCATGACGTTTTTCTTCCTGGCGCTGTGGGGGCCCTATCTGGTCGCCTGCTACTGGCGGGTGTTTGCCAGGGGCCCCGTGGTCCCTGGGGGCTACCTGACGGCAGCCGTGTGGATGAGCTTTGCCCAGGCTGGGGTCAATCCTTTCATCTGC

[Andy]

Haven't used IMa2 yet, but in IM, each allele should be on it's own
line with its own name. Forget about individuals, the unit of analysis
is the allele. It seems that you are grouping both alleles under one
name which is the problem.

One individual should be coded like:

indiv001_a AAATTCTCC...
indiv002_b AAAATCTCG...

etc.

Hope that solves your problem. Any little error in the input file can
cause the program to crash.

Andy

[Justin Lewandowski]

That actually ended up what it was. Thanks a ton!!