>2.975e-13
CTGTTTGTTTATGTCACACACAGACAAACAC
>2.621e-13
CTTCACCACACATGTGTGTATTGTGGAGTGA
>3.308e-13
CTTCAGATGGTATGCTCTCCAATTGATGTCA
... (+ 60 more kmers)
I am using a slurm HPC cluster so I have plenty of available memory!
The highlighted line in yellow is my code and the error is written in bold.
ABYSS -k31 -c0 -e0 input.txt -o output.txt
ABySS 2.0.2
ABYSS -k31 -c0 -e0 input.txt -o output.txt
Reading `input.txt'...
Loaded 63 k-mer
Unable to determine minimum k-mer coverage
Using a coverage threshold of 1...
The median k-mer coverage is 1
The reconstruction is 63
The k-mer coverage threshold is 1
Setting parameter E (erodeStrand) to 0
Generating adjacency
Added 20 edges.
Pruning tips shorter than 1 bp...
Pruned 45 k-mer in 45 tips.
Pruning tips shorter than 2 bp...
Pruned 14 k-mer in 14 tips.
Pruning tips shorter than 4 bp...
Pruned 4 k-mer in 2 tips.
Pruning tips shorter than 8 bp...
Pruning tips shorter than 16 bp...
Pruning tips shorter than 31 bp...
Pruned 61 tips in 5 rounds.
Popping bubbles
Removed 0 bubbles
Marked 0 edges of 0 ambiguous vertices.
Assembled 0 k-mer in 0 contigs.
error: no contigs assembled
Thanks in advance for your help.
Amin