Hi,
I'm keep getting the invalid seed message when I use the "mito" program, regardless of the seed that I use (I have tried many). I know my files have mitochondrial reads in them, as I have previously aligned these to a reference genome, and that I have high coverage. Here is my log file (the extended doesn't seem to have much information in it):
Project:
Project name = test
Type = mito
Genome range = 12000-22000
K-mer = 33
Max memory =
Extended log = 1
Save assembled reads = no
Seed Input = sequence.fasta
Extend seed directly = no
Reference sequence =
Variance detection =
Chloroplast sequence =
Subsampled fraction: 90.97 %
Forward reads without pair: 26
Reverse reads without pair: 0
Retrieve Seed...
INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE
The seed is:
MT882033.1
CAAAGGTAGCATAATAATTTGTTTTTTAATTGGAAACTAGTATGAATGGTCATACGAGGGATTGACTTTC
TTTATCTTACTTAAATTAATTTTATTTTTCTGTGAAAAAGCAGAGATTTCATTAGTAGACGATAAGACCC
TTTAAAACTTTATTCATTATAGAAGTATAATTTTGTTAGGTTTTAATAGTGTACTTTTTTAATGAGTTTT
GTTGGGGCGACAGGTAAATTTATTTAACTTTATTTTTGTTTTTCACTAATTAGTGTTTATTTGATCCAGA
TTTAGTTTTGATTATAAGTTTAAGTTACTT
Can you advise?
Hi, I'm keep getting the invalid seed message when I use the "mito" program, regardless of the seed that I use (I have tried many). I know my files have mitochondrial reads in them, as I have previously aligned these to a reference genome, and that I have high coverage. Here is my log file (the extended doesn't seem to have much information in it):
Project:
Project name = test Type = mito Genome range = 12000-22000 K-mer = 33 Max memory = Extended log = 1 Save assembled reads = no Seed Input = sequence.fasta Extend seed directly = no Reference sequence = Variance detection = Chloroplast sequence =
Dataset 1:
Read Length = 250 Insert size = 500 Platform = illumina Single/Paired = PE Combined reads = Forward reads = reads_1.fastq Reverse reads = reads_2.fastq
Heteroplasmy:
Heteroplasmy = HP exclude list = PCR-free =
Optional:
Insert size auto = yes Use Quality Scores =
Subsampled fraction: 90.97 % Forward reads without pair: 26 Reverse reads without pair: 0
Retrieve Seed...
INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE
The seed is:
Thanks,
Brenna